| 1 |
- #' Generate lockfile for application's environment reproducibility+ #' `teal` main module |
||
| 3 |
- #' @param lockfile_path (`character`) path to the lockfile.+ #' @description |
||
| 4 |
- #'+ #' `r lifecycle::badge("stable")`
|
||
| 5 |
- #' @section Different ways of creating lockfile:+ #' Module to create a `teal` app. This module can be called directly instead of [init()] and |
||
| 6 |
- #' `teal` leverages [renv::snapshot()], which offers multiple methods for lockfile creation.+ #' included in your custom application. Please note that [init()] adds `reporter_previewer_module` |
||
| 7 |
- #'+ #' automatically, which is not a case when calling `ui/srv_teal` directly. |
||
| 8 |
- #' - **Working directory lockfile**: `teal`, by default, will create an `implicit` type lockfile that uses+ #' |
||
| 9 |
- #' `renv::dependencies()` to detect all R packages in the current project's working directory.+ #' @details |
||
| 10 |
- #' - **`DESCRIPTION`-based lockfile**: To generate a lockfile based on a `DESCRIPTION` file in your working+ #' |
||
| 11 |
- #' directory, set `renv::settings$snapshot.type("explicit")`. The naming convention for `type` follows
+ #' Module is responsible for creating the main `shiny` app layout and initializing all the necessary |
||
| 12 |
- #' `renv::snapshot()`. For the `"explicit"` type, refer to `renv::settings$package.dependency.fields()` for the+ #' components. This module establishes reactive connection between the input `data` and every other |
||
| 13 |
- #' `DESCRIPTION` fields included in the lockfile.+ #' component in the app. Reactive change of the `data` passed as an argument, reloads the app and |
||
| 14 |
- #' - **Custom files-based lockfile**: To specify custom files as the basis for the lockfile, set+ #' possibly keeps all input settings the same so the user can continue where one left off. |
||
| 15 |
- #' `renv::settings$snapshot.type("custom")` and configure the `renv.snapshot.filter` option.
+ #' |
||
| 16 |
- #'+ #' ## data flow in `teal` application |
||
| 17 |
- #' @section lockfile usage:+ #' |
||
| 18 |
- #' After creating the lockfile, you can restore the application's environment using `renv::restore()`.+ #' This module supports multiple data inputs but eventually, they are all converted to `reactive` |
||
| 19 |
- #'+ #' returning `teal_data` in this module. On this `reactive teal_data` object several actions are |
||
| 20 |
- #' @seealso [renv::snapshot()], [renv::restore()].+ #' performed: |
||
| 21 |
- #'+ #' - data loading in [`module_init_data`] |
||
| 22 |
- #' @return `NULL`+ #' - data filtering in [`module_filter_data`] |
||
| 23 |
- #'+ #' - data transformation in [`module_transform_data`] |
||
| 24 |
- #' @name module_teal_lockfile+ #' |
||
| 25 |
- #' @rdname module_teal_lockfile+ #' ## Fallback on failure |
||
| 27 |
- #' @keywords internal+ #' `teal` is designed in such way that app will never crash if the error is introduced in any |
||
| 28 |
- NULL+ #' custom `shiny` module provided by app developer (e.g. [teal_data_module()], [teal_transform_module()]). |
||
| 29 |
-
+ #' If any module returns a failing object, the app will halt the evaluation and display a warning message. |
||
| 30 |
- #' @rdname module_teal_lockfile+ #' App user should always have a chance to fix the improper input and continue without restarting the session. |
||
| 31 |
- ui_teal_lockfile <- function(id) {
+ #' |
||
| 32 | -! | +
- ns <- NS(id)+ #' @rdname module_teal |
|
| 33 | -! | +
- shiny::tagList(+ #' @name module_teal |
|
| 34 | -! | +
- tags$span("", id = ns("lockFileStatus")),
+ #' |
|
| 35 | -! | +
- shinyjs::disabled(downloadLink(ns("lockFileLink"), "Download lockfile"))
+ #' @inheritParams module_init_data |
|
| 36 |
- )+ #' @inheritParams init |
||
| 37 |
- }+ #' |
||
| 38 |
-
+ #' @return `NULL` invisibly |
||
| 39 |
- #' @rdname module_teal_lockfile+ NULL |
||
| 40 |
- srv_teal_lockfile <- function(id) {
+
|
||
| 41 | -88x | +
- moduleServer(id, function(input, output, session) {
+ #' @rdname module_teal |
|
| 42 | -88x | +
- logger::log_debug("Initialize srv_teal_lockfile.")
+ #' @export |
|
| 43 | -88x | +
- enable_lockfile_download <- function() {
+ ui_teal <- function(id, |
|
| 44 | -! | +
- shinyjs::html("lockFileStatus", "Application lockfile ready.")
+ modules, |
|
| 45 | -! | +
- shinyjs::hide("lockFileStatus", anim = TRUE)
+ title = build_app_title(), |
|
| 46 | -! | +
- shinyjs::enable("lockFileLink")
+ header = tags$p(), |
|
| 47 | -! | +
- output$lockFileLink <- shiny::downloadHandler(+ footer = tags$p()) {
|
|
| 48 | ! |
- filename = function() {
+ checkmate::assert_character(id, max.len = 1, any.missing = FALSE) |
|
| 49 | ! |
- "renv.lock"+ checkmate::assert( |
|
| 50 | -+ | ! |
- },+ .var.name = "title", |
| 51 | ! |
- content = function(file) {
+ checkmate::check_string(title), |
|
| 52 | ! |
- file.copy(lockfile_path, file)+ checkmate::check_multi_class(title, c("shiny.tag", "shiny.tag.list", "html"))
|
|
| 53 | -! | +
- file+ ) |
|
| 54 | -+ | ! |
- },+ checkmate::assert( |
| 55 | ! |
- contentType = "application/json"+ .var.name = "header", |
|
| 56 | -+ | ! |
- )+ checkmate::check_string(header), |
| 57 | -+ | ! |
- }+ checkmate::check_multi_class(header, c("shiny.tag", "shiny.tag.list", "html"))
|
| 58 | -88x | +
- disable_lockfile_download <- function() {
+ ) |
|
| 59 | ! |
- warning("Lockfile creation failed.", call. = FALSE)
+ checkmate::assert( |
|
| 60 | ! |
- shinyjs::html("lockFileStatus", "Lockfile creation failed.")
+ .var.name = "footer", |
|
| 61 | ! |
- shinyjs::hide("lockFileLink")
+ checkmate::check_string(footer), |
|
| 62 | -+ | ! |
- }+ checkmate::check_multi_class(footer, c("shiny.tag", "shiny.tag.list", "html"))
|
| 63 |
-
+ ) |
||
| 64 | -88x | +
- shiny::onStop(function() {
+
|
|
| 65 | -88x | +! |
- if (file.exists(lockfile_path) && !shiny::isRunning()) {
+ if (is.character(title)) {
|
| 66 | -1x | +! |
- logger::log_debug("Removing lockfile after shutting down the app")
+ title <- build_app_title(title) |
| 67 | -1x | +
- file.remove(lockfile_path)+ } else {
|
|
| 68 | -+ | ! |
- }+ validate_app_title_tag(title) |
| 69 |
- })+ } |
||
| 71 | -88x | +! |
- lockfile_path <- "teal_app.lock"+ if (checkmate::test_string(header)) {
|
| 72 | -88x | +! |
- mode <- getOption("teal.lockfile.mode", default = "")
+ header <- tags$p(header) |
| 73 |
-
+ } |
||
| 74 | -88x | +
- if (!(mode %in% c("auto", "enabled", "disabled"))) {
+
|
|
| 75 | ! |
- stop("'teal.lockfile.mode' option can only be one of \"auto\", \"disabled\" or \"disabled\". ")
+ if (checkmate::test_string(footer)) {
|
|
| 76 | -+ | ! |
- }+ footer <- tags$p(footer) |
| 77 |
-
+ } |
||
| 78 | -88x | +
- if (mode == "disabled") {
+
|
|
| 79 | -1x | +! |
- logger::log_debug("'teal.lockfile.mode' option is set to 'disabled'. Hiding lockfile download button.")
+ ns <- NS(id) |
| 80 | -1x | +
- shinyjs::hide("lockFileLink")
+
|
|
| 81 | -1x | +
- return(NULL)+ # show busy icon when `shiny` session is busy computing stuff |
|
| 82 |
- }+ # based on https://stackoverflow.com/questions/17325521/r-shiny-display-loading-message-while-function-is-running/22475216#22475216 # nolint: line_length. |
||
| 83 | -+ | ! |
-
+ shiny_busy_message_panel <- conditionalPanel( |
| 84 | -87x | +! |
- if (file.exists(lockfile_path)) {
+ condition = "(($('html').hasClass('shiny-busy')) && (document.getElementById('shiny-notification-panel') == null))", # nolint: line_length.
|
| 85 | ! |
- logger::log_debug("Lockfile has already been created for this app - skipping automatic creation.")
+ tags$div( |
|
| 86 | ! |
- enable_lockfile_download()+ icon("arrows-rotate", class = "fa-spin", prefer_type = "solid"),
|
|
| 87 | ! |
- return(NULL)+ "Computing ...", |
|
| 88 |
- }+ # CSS defined in `custom.css` |
||
| 89 | -+ | ! |
-
+ class = "shinybusymessage" |
| 90 | -87x | +
- if (mode == "auto" && .is_disabled_lockfile_scenario()) {
+ ) |
|
| 91 | -86x | +
- logger::log_debug(+ ) |
|
| 92 | -86x | +
- "Automatic lockfile creation disabled. Execution scenario satisfies teal:::.is_disabled_lockfile_scenario()."+ |
|
| 93 | -+ | ! |
- )+ fluidPage( |
| 94 | -86x | +! |
- shinyjs::hide("lockFileLink")
+ id = id, |
| 95 | -86x | +! |
- return(NULL)+ title = title, |
| 96 | -+ | ! |
- }+ theme = get_teal_bs_theme(), |
| 97 | -+ | ! |
-
+ include_teal_css_js(), |
| 98 | -1x | +! |
- if (!.is_lockfile_deps_installed()) {
+ tags$header(header), |
| 99 | ! |
- warning("Automatic lockfile creation disabled. `mirai` and `renv` packages must be installed.")
+ tags$hr(class = "my-2"), |
|
| 100 | ! |
- shinyjs::hide("lockFileLink")
+ shiny_busy_message_panel, |
|
| 101 | ! |
- return(NULL)+ tags$div( |
|
| 102 | -+ | ! |
- }+ id = ns("tabpanel_wrapper"),
|
| 103 | -+ | ! |
-
+ class = "teal-body", |
| 104 | -+ | ! |
- # - Will be run only if the lockfile doesn't exist (see the if-s above)+ ui_teal_module(id = ns("teal_modules"), modules = modules)
|
| 105 |
- # - We render to the tempfile because the process might last after session is closed and we don't+ ), |
||
| 106 | -+ | ! |
- # want to make a "teal_app.renv" then. This is why we copy only during active session.+ tags$div( |
| 107 | -1x | +! |
- process <- .teal_lockfile_process_invoke(lockfile_path)+ id = ns("options_buttons"),
|
| 108 | -1x | +! |
- observeEvent(process$status(), {
+ style = "position: absolute; right: 10px;", |
| 109 | ! |
- if (process$status() %in% c("initial", "running")) {
+ ui_bookmark_panel(ns("bookmark_manager"), modules),
|
|
| 110 | ! |
- shinyjs::html("lockFileStatus", "Creating lockfile...")
+ tags$button( |
|
| 111 | ! |
- } else if (process$status() == "success") {
+ class = "btn action-button filter_hamburger", # see sidebar.css for style filter_hamburger |
|
| 112 | ! |
- result <- process$result()+ href = "javascript:void(0)", |
|
| 113 | ! |
- if (any(grepl("Lockfile written to", result$out))) {
+ onclick = sprintf("toggleFilterPanel('%s');", ns("tabpanel_wrapper")),
|
|
| 114 | ! |
- logger::log_debug("Lockfile containing { length(result$res$Packages) } packages created.")
+ title = "Toggle filter panel", |
|
| 115 | ! |
- if (any(grepl("(WARNING|ERROR):", result$out))) {
+ icon("fas fa-bars")
|
|
| 116 | -! | +
- warning("Lockfile created with warning(s) or error(s):", call. = FALSE)
+ ), |
|
| 117 | ! |
- for (i in result$out) {
+ ui_snapshot_manager_panel(ns("snapshot_manager_panel")),
|
|
| 118 | ! |
- warning(i, call. = FALSE)+ ui_filter_manager_panel(ns("filter_manager_panel"))
|
|
| 119 |
- }+ ), |
||
| 120 | -+ | ! |
- }+ tags$script( |
| 121 | ! |
- enable_lockfile_download()+ HTML( |
|
| 122 | -+ | ! |
- } else {
+ sprintf( |
| 123 | -! | +
- disable_lockfile_download()+ " |
|
| 124 | -+ | ! |
- }+ $(document).ready(function() {
|
| 125 | ! |
- } else if (process$status() == "error") {
+ $('#%s').appendTo('#%s');
|
|
| 126 | -! | +
- disable_lockfile_download()+ }); |
|
| 127 |
- }+ ", |
||
| 128 | -+ | ! |
- })+ ns("options_buttons"),
|
| 129 | -+ | ! |
-
+ ns("teal_modules-active_tab")
|
| 130 | -1x | +
- NULL+ ) |
|
| 131 |
- })+ ) |
||
| 132 |
- }+ ), |
||
| 133 | -+ | ! |
-
+ tags$hr(), |
| 134 | -+ | ! |
- utils::globalVariables(c("opts", "sysenv", "libpaths", "wd", "lockfilepath", "run")) # needed for mirai call
+ tags$footer( |
| 135 | -+ | ! |
- #' @rdname module_teal_lockfile+ tags$div( |
| 136 | -+ | ! |
- .teal_lockfile_process_invoke <- function(lockfile_path) {
+ footer, |
| 137 | -1x | +! |
- mirai_obj <- NULL+ teal.widgets::verbatim_popup_ui(ns("sessionInfo"), "Session Info", type = "link"),
|
| 138 | -1x | +! |
- process <- shiny::ExtendedTask$new(function() {
+ br(), |
| 139 | -1x | +! |
- m <- mirai::mirai(+ ui_teal_lockfile(ns("lockfile")),
|
| 140 | -+ | ! |
- {
+ textOutput(ns("identifier"))
|
| 141 | -1x | +
- options(opts)+ ) |
|
| 142 | -1x | +
- do.call(Sys.setenv, sysenv)+ ) |
|
| 143 | -1x | +
- .libPaths(libpaths)+ ) |
|
| 144 | -1x | +
- setwd(wd)+ } |
|
| 145 | -1x | +
- run(lockfile_path = lockfile_path)+ |
|
| 146 |
- },+ #' @rdname module_teal |
||
| 147 | -1x | +
- run = .renv_snapshot,+ #' @export |
|
| 148 | -1x | +
- lockfile_path = lockfile_path,+ srv_teal <- function(id, data, modules, filter = teal_slices()) {
|
|
| 149 | -1x | +89x |
- opts = options(),+ checkmate::assert_character(id, max.len = 1, any.missing = FALSE) |
| 150 | -1x | +89x |
- libpaths = .libPaths(),+ checkmate::assert_multi_class(data, c("teal_data", "teal_data_module", "reactive"))
|
| 151 | -1x | +88x |
- sysenv = as.list(Sys.getenv()),+ checkmate::assert_class(modules, "teal_modules") |
| 152 | -1x | +88x |
- wd = getwd()+ checkmate::assert_class(filter, "teal_slices") |
| 153 |
- )+ |
||
| 154 | -1x | +88x |
- mirai_obj <<- m+ moduleServer(id, function(input, output, session) {
|
| 155 | -1x | +88x |
- m+ logger::log_debug("srv_teal initializing.")
|
| 156 |
- })+ |
||
| 157 | -+ | 88x |
-
+ if (getOption("teal.show_js_log", default = FALSE)) {
|
| 158 | -1x | +! |
- shiny::onStop(function() {
+ shinyjs::showLog() |
| 159 | -1x | +
- if (mirai::unresolved(mirai_obj)) {
+ } |
|
| 160 | -! | +
- logger::log_debug("Terminating a running lockfile process...")
+
|
|
| 161 | -! | +88x |
- mirai::stop_mirai(mirai_obj) # this doesn't stop running - renv will be created even if session is closed+ srv_teal_lockfile("lockfile")
|
| 162 |
- }+ |
||
| 163 | -+ | 88x |
- })+ output$identifier <- renderText( |
| 164 | -+ | 88x |
-
+ paste0("Pid:", Sys.getpid(), " Token:", substr(session$token, 25, 32))
|
| 165 | -1x | +
- suppressWarnings({ # 'package:stats' may not be available when loading
+ ) |
|
| 166 | -1x | +
- process$invoke()+ |
|
| 167 | -+ | 88x |
- })+ teal.widgets::verbatim_popup_srv( |
| 168 | -+ | 88x |
-
+ "sessionInfo", |
| 169 | -1x | +88x |
- logger::log_debug("Lockfile creation started based on { getwd() }.")
+ verbatim_content = utils::capture.output(utils::sessionInfo()), |
| 170 | -+ | 88x |
-
+ title = "SessionInfo" |
| 171 | -1x | +
- process+ ) |
|
| 172 |
- }+ |
||
| 173 |
-
+ # `JavaScript` code |
||
| 174 | -+ | 88x |
- #' @rdname module_teal_lockfile+ run_js_files(files = "init.js") |
| 175 |
- .renv_snapshot <- function(lockfile_path) {
+
|
||
| 176 | -1x | +
- out <- utils::capture.output(+ # set timezone in shiny app |
|
| 177 | -1x | +
- res <- renv::snapshot(+ # timezone is set in the early beginning so it will be available also |
|
| 178 | -1x | +
- lockfile = lockfile_path,+ # for `DDL` and all shiny modules |
|
| 179 | -1x | +88x |
- prompt = FALSE,+ get_client_timezone(session$ns) |
| 180 | -1x | +88x |
- force = TRUE,+ observeEvent( |
| 181 | -1x | +88x |
- type = renv::settings$snapshot.type() # see the section "Different ways of creating lockfile" above here+ eventExpr = input$timezone, |
| 182 | -+ | 88x |
- )+ once = TRUE, |
| 183 | -+ | 88x |
- )+ handlerExpr = {
|
| 184 | -+ | ! |
-
+ session$userData$timezone <- input$timezone |
| 185 | -1x | +! |
- list(out = out, res = res)+ logger::log_debug("srv_teal@1 Timezone set to client's timezone: { input$timezone }.")
|
| 186 |
- }+ } |
||
| 187 |
-
+ ) |
||
| 188 |
- #' @rdname module_teal_lockfile+ |
||
| 189 | -+ | 88x |
- .is_lockfile_deps_installed <- function() {
+ data_handled <- srv_init_data("data", data = data)
|
| 190 | -1x | +
- requireNamespace("mirai", quietly = TRUE) && requireNamespace("renv", quietly = TRUE)
+
|
|
| 191 | -+ | 87x |
- }+ validate_ui <- tags$div( |
| 192 | -+ | 87x |
-
+ id = session$ns("validate_messages"),
|
| 193 | -+ | 87x |
- #' @rdname module_teal_lockfile+ class = "teal_validated", |
| 194 | -+ | 87x |
- .is_disabled_lockfile_scenario <- function() {
+ ui_check_class_teal_data(session$ns("class_teal_data")),
|
| 195 | -86x | +87x |
- identical(Sys.getenv("CALLR_IS_RUNNING"), "true") || # inside callr process
+ ui_validate_error(session$ns("silent_error")),
|
| 196 | -86x | +87x |
- identical(Sys.getenv("TESTTHAT"), "true") || # inside devtools::test
+ ui_check_module_datanames(session$ns("datanames_warning"))
|
| 197 | -86x | +
- !identical(Sys.getenv("QUARTO_PROJECT_ROOT"), "") || # inside Quarto process
+ ) |
|
| 198 | -+ | 87x |
- (+ srv_check_class_teal_data("class_teal_data", data_handled)
|
| 199 | -86x | +87x |
- ("CheckExEnv" %in% search()) || any(c("_R_CHECK_TIMINGS_", "_R_CHECK_LICENSE_") %in% names(Sys.getenv()))
+ srv_validate_error("silent_error", data_handled, validate_shiny_silent_error = FALSE)
|
| 200 | -86x | +87x |
- ) # inside R CMD CHECK+ srv_check_module_datanames("datanames_warning", data_handled, modules)
|
| 201 |
- }+ |
| 1 | -+ | ||
| 202 | +87x |
- #' `teal` main module+ data_validated <- .trigger_on_success(data_handled) |
|
| 2 | +203 |
- #'+ |
|
| 3 | -+ | ||
| 204 | +87x |
- #' @description+ data_signatured <- reactive({
|
|
| 4 | -+ | ||
| 205 | +152x |
- #' `r lifecycle::badge("stable")`
+ req(inherits(data_validated(), "teal_data")) |
|
| 5 | -+ | ||
| 206 | +75x |
- #' Module to create a `teal` app. This module can be called directly instead of [init()] and+ is_filter_ok <- check_filter_datanames(filter, names(data_validated())) |
|
| 6 | -+ | ||
| 207 | +75x |
- #' included in your custom application. Please note that [init()] adds `reporter_previewer_module`+ if (!isTRUE(is_filter_ok)) {
|
|
| 7 | -+ | ||
| 208 | +2x |
- #' automatically, which is not a case when calling `ui/srv_teal` directly.+ showNotification( |
|
| 8 | -+ | ||
| 209 | +2x |
- #'+ "Some filters were not applied because of incompatibility with data. Contact app developer.", |
|
| 9 | -+ | ||
| 210 | +2x |
- #' @details+ type = "warning", |
|
| 10 | -+ | ||
| 211 | +2x |
- #'+ duration = 10 |
|
| 11 | +212 |
- #' Module is responsible for creating the main `shiny` app layout and initializing all the necessary+ ) |
|
| 12 | -+ | ||
| 213 | +2x |
- #' components. This module establishes reactive connection between the input `data` and every other+ warning(is_filter_ok) |
|
| 13 | +214 |
- #' component in the app. Reactive change of the `data` passed as an argument, reloads the app and+ } |
|
| 14 | -+ | ||
| 215 | +75x |
- #' possibly keeps all input settings the same so the user can continue where one left off.+ .add_signature_to_data(data_validated()) |
|
| 15 | +216 |
- #'+ }) |
|
| 16 | +217 |
- #' ## data flow in `teal` application+ |
|
| 17 | -+ | ||
| 218 | +87x |
- #'+ data_load_status <- reactive({
|
|
| 18 | -+ | ||
| 219 | +80x |
- #' This module supports multiple data inputs but eventually, they are all converted to `reactive`+ if (inherits(data_handled(), "teal_data")) {
|
|
| 19 | -+ | ||
| 220 | +75x |
- #' returning `teal_data` in this module. On this `reactive teal_data` object several actions are+ "ok" |
|
| 20 | -+ | ||
| 221 | +5x |
- #' performed:+ } else if (inherits(data, "teal_data_module")) {
|
|
| 21 | -+ | ||
| 222 | +5x |
- #' - data loading in [`module_init_data`]+ "teal_data_module failed" |
|
| 22 | +223 |
- #' - data filtering in [`module_filter_data`]+ } else {
|
|
| 23 | -+ | ||
| 224 | +! |
- #' - data transformation in [`module_transform_data`]+ "external failed" |
|
| 24 | +225 |
- #'+ } |
|
| 25 | +226 |
- #' ## Fallback on failure+ }) |
|
| 26 | +227 |
- #'+ |
|
| 27 | -+ | ||
| 228 | +87x |
- #' `teal` is designed in such way that app will never crash if the error is introduced in any+ datasets_rv <- if (!isTRUE(attr(filter, "module_specific"))) {
|
|
| 28 | -+ | ||
| 229 | +76x |
- #' custom `shiny` module provided by app developer (e.g. [teal_data_module()], [teal_transform_module()]).+ eventReactive(data_signatured(), {
|
|
| 29 | -+ | ||
| 230 | +66x |
- #' If any module returns a failing object, the app will halt the evaluation and display a warning message.+ req(inherits(data_signatured(), "teal_data")) |
|
| 30 | -+ | ||
| 231 | +66x |
- #' App user should always have a chance to fix the improper input and continue without restarting the session.+ logger::log_debug("srv_teal@1 initializing FilteredData")
|
|
| 31 | -+ | ||
| 232 | +66x |
- #'+ teal_data_to_filtered_data(data_signatured()) |
|
| 32 | +233 |
- #' @rdname module_teal+ }) |
|
| 33 | +234 |
- #' @name module_teal+ } |
|
| 34 | +235 |
- #'+ |
|
| 35 | +236 |
- #' @inheritParams module_init_data+ |
|
| 36 | +237 |
- #' @inheritParams init+ + |
+ |
| 238 | +87x | +
+ if (inherits(data, "teal_data_module")) {
+ |
+ |
| 239 | +9x | +
+ setBookmarkExclude(c("teal_modules-active_tab"))
+ |
+ |
| 240 | +9x | +
+ shiny::insertTab(+ |
+ |
| 241 | +9x | +
+ inputId = "teal_modules-active_tab",+ |
+ |
| 242 | +9x | +
+ position = "before",+ |
+ |
| 243 | +9x | +
+ select = TRUE,+ |
+ |
| 244 | +9x | +
+ tabPanel(+ |
+ |
| 245 | +9x | +
+ title = icon("fas fa-database"),
+ |
+ |
| 246 | +9x | +
+ value = "teal_data_module",+ |
+ |
| 247 | +9x | +
+ tags$div(+ |
+ |
| 248 | +9x | +
+ ui_init_data(session$ns("data")),
+ |
+ |
| 249 | +9x | +
+ validate_ui |
|
| 37 | +250 |
- #'+ ) |
|
| 38 | +251 |
- #' @return `NULL` invisibly+ ) |
|
| 39 | +252 |
- NULL+ ) |
|
| 40 | +253 | ||
| 41 | -+ | ||
| 254 | +9x |
- #' @rdname module_teal+ if (attr(data, "once")) {
|
|
| 42 | -+ | ||
| 255 | +9x |
- #' @export+ observeEvent(data_signatured(), once = TRUE, {
+ |
+ |
| 256 | +4x | +
+ logger::log_debug("srv_teal@2 removing data tab.")
|
|
| 43 | +257 |
- ui_teal <- function(id,+ # when once = TRUE we pull data once and then remove data tab+ |
+ |
| 258 | +4x | +
+ removeTab("teal_modules-active_tab", target = "teal_data_module")
|
|
| 44 | +259 |
- modules,+ }) |
|
| 45 | +260 |
- title = build_app_title(),+ } |
|
| 46 | +261 |
- header = tags$p(),+ } else {
|
|
| 47 | +262 |
- footer = tags$p()) {
+ # when no teal_data_module then we want to display messages above tabsetPanel (because there is no data-tab) |
|
| 48 | -! | +||
| 263 | +78x |
- checkmate::assert_character(id, max.len = 1, any.missing = FALSE)+ insertUI( |
|
| 49 | -! | +||
| 264 | +78x |
- checkmate::assert(+ selector = sprintf("#%s", session$ns("tabpanel_wrapper")),
|
|
| 50 | -! | +||
| 265 | +78x |
- .var.name = "title",+ where = "beforeBegin", |
|
| 51 | -! | +||
| 266 | +78x |
- checkmate::check_string(title),+ ui = tags$div(validate_ui, tags$br()) |
|
| 52 | -! | +||
| 267 | +
- checkmate::check_multi_class(title, c("shiny.tag", "shiny.tag.list", "html"))
+ ) |
||
| 53 | +268 |
- )+ } |
|
| 54 | -! | +||
| 269 | +
- checkmate::assert(+ |
||
| 55 | -! | +||
| 270 | +87x |
- .var.name = "header",+ module_labels <- unlist(module_labels(modules), use.names = FALSE) |
|
| 56 | -! | +||
| 271 | +87x |
- checkmate::check_string(header),+ slices_global <- methods::new(".slicesGlobal", filter, module_labels)
|
|
| 57 | -! | +||
| 272 | +87x |
- checkmate::check_multi_class(header, c("shiny.tag", "shiny.tag.list", "html"))
+ modules_output <- srv_teal_module( |
|
| 58 | -+ | ||
| 273 | +87x |
- )+ id = "teal_modules", |
|
| 59 | -! | +||
| 274 | +87x |
- checkmate::assert(+ data = data_signatured, |
|
| 60 | -! | +||
| 275 | +87x |
- .var.name = "footer",+ datasets = datasets_rv, |
|
| 61 | -! | +||
| 276 | +87x |
- checkmate::check_string(footer),+ modules = modules, |
|
| 62 | -! | +||
| 277 | +87x |
- checkmate::check_multi_class(footer, c("shiny.tag", "shiny.tag.list", "html"))
+ slices_global = slices_global, |
|
| 63 | -+ | ||
| 278 | +87x |
- )+ data_load_status = data_load_status |
|
| 64 | +279 | - - | -|
| 65 | -! | -
- if (is.character(title)) {
+ ) |
|
| 66 | -! | +||
| 280 | +87x |
- title <- build_app_title(title)+ mapping_table <- srv_filter_manager_panel("filter_manager_panel", slices_global = slices_global)
|
|
| 67 | -+ | ||
| 281 | +87x |
- } else {
+ snapshots <- srv_snapshot_manager_panel("snapshot_manager_panel", slices_global = slices_global)
|
|
| 68 | -! | +||
| 282 | +87x |
- validate_app_title_tag(title)+ srv_bookmark_panel("bookmark_manager", modules)
|
|
| 69 | +283 |
- }+ }) |
|
| 70 | +284 | ||
| 71 | -! | +||
| 285 | +87x |
- if (checkmate::test_string(header)) {
+ invisible(NULL) |
|
| 72 | -! | +||
| 286 | +
- header <- tags$p(header)+ } |
| 73 | +1 |
- }+ #' Calls all `modules` |
||
| 74 | +2 |
-
+ #' |
||
| 75 | -! | +|||
| 3 | +
- if (checkmate::test_string(footer)) {
+ #' On the UI side each `teal_modules` is translated to a `tabsetPanel` and each `teal_module` is a |
|||
| 76 | -! | +|||
| 4 | +
- footer <- tags$p(footer)+ #' `tabPanel`. Both, UI and server are called recursively so that each tab is a separate module and |
|||
| 77 | +5 |
- }+ #' reflect nested structure of `modules` argument. |
||
| 78 | +6 |
-
+ #' |
||
| 79 | -! | +|||
| 7 | +
- ns <- NS(id)+ #' @name module_teal_module |
|||
| 80 | +8 |
-
+ #' |
||
| 81 | +9 |
- # show busy icon when `shiny` session is busy computing stuff+ #' @inheritParams module_teal |
||
| 82 | +10 |
- # based on https://stackoverflow.com/questions/17325521/r-shiny-display-loading-message-while-function-is-running/22475216#22475216 # nolint: line_length.+ #' |
||
| 83 | -! | +|||
| 11 | +
- shiny_busy_message_panel <- conditionalPanel(+ #' @param data (`reactive` returning `teal_data`) |
|||
| 84 | -! | +|||
| 12 | +
- condition = "(($('html').hasClass('shiny-busy')) && (document.getElementById('shiny-notification-panel') == null))", # nolint: line_length.
+ #' |
|||
| 85 | -! | +|||
| 13 | +
- tags$div(+ #' @param slices_global (`reactiveVal` returning `modules_teal_slices`) |
|||
| 86 | -! | +|||
| 14 | +
- icon("arrows-rotate", class = "fa-spin", prefer_type = "solid"),
+ #' see [`module_filter_manager`] |
|||
| 87 | -! | +|||
| 15 | +
- "Computing ...",+ #' |
|||
| 88 | +16 |
- # CSS defined in `custom.css`+ #' @param depth (`integer(1)`) |
||
| 89 | -! | +|||
| 17 | +
- class = "shinybusymessage"+ #' number which helps to determine depth of the modules nesting. |
|||
| 90 | +18 |
- )+ #' |
||
| 91 | +19 |
- )+ #' @param datasets (`reactive` returning `FilteredData` or `NULL`) |
||
| 92 | +20 |
-
+ #' When `datasets` is passed from the parent module (`srv_teal`) then `dataset` is a singleton |
||
| 93 | -! | +|||
| 21 | +
- fluidPage(+ #' which implies in filter-panel to be "global". When `NULL` then filter-panel is "module-specific". |
|||
| 94 | -! | +|||
| 22 | +
- id = id,+ #' |
|||
| 95 | -! | +|||
| 23 | +
- title = title,+ #' @param data_load_status (`reactive` returning `character`) |
|||
| 96 | -! | +|||
| 24 | +
- theme = get_teal_bs_theme(),+ #' Determines action dependent on a data loading status: |
|||
| 97 | -! | +|||
| 25 | +
- include_teal_css_js(),+ #' - `"ok"` when `teal_data` is returned from the data loading. |
|||
| 98 | -! | +|||
| 26 | +
- tags$header(header),+ #' - `"teal_data_module failed"` when [teal_data_module()] didn't return `teal_data`. Disables tabs buttons. |
|||
| 99 | -! | +|||
| 27 | +
- tags$hr(class = "my-2"),+ #' - `"external failed"` when a `reactive` passed to `srv_teal(data)` didn't return `teal_data`. Hides the whole tab |
|||
| 100 | -! | +|||
| 28 | +
- shiny_busy_message_panel,+ #' panel. |
|||
| 101 | -! | +|||
| 29 | +
- tags$div(+ #' |
|||
| 102 | -! | +|||
| 30 | +
- id = ns("tabpanel_wrapper"),
+ #' @return |
|||
| 103 | -! | +|||
| 31 | +
- class = "teal-body",+ #' output of currently active module. |
|||
| 104 | -! | +|||
| 32 | +
- ui_teal_module(id = ns("teal_modules"), modules = modules)
+ #' - `srv_teal_module.teal_module` returns `reactiveVal` containing output of the called module. |
|||
| 105 | +33 |
- ),+ #' - `srv_teal_module.teal_modules` returns output of module selected by `input$active_tab`. |
||
| 106 | -! | +|||
| 34 | +
- tags$div(+ #' |
|||
| 107 | -! | +|||
| 35 | +
- id = ns("options_buttons"),
+ #' @keywords internal |
|||
| 108 | -! | +|||
| 36 | +
- style = "position: absolute; right: 10px;",+ NULL |
|||
| 109 | -! | +|||
| 37 | +
- ui_bookmark_panel(ns("bookmark_manager"), modules),
+
|
|||
| 110 | -! | +|||
| 38 | +
- tags$button(+ #' @rdname module_teal_module |
|||
| 111 | -! | +|||
| 39 | +
- class = "btn action-button filter_hamburger", # see sidebar.css for style filter_hamburger+ ui_teal_module <- function(id, modules, depth = 0L) {
|
|||
| 112 | +40 | ! |
- href = "javascript:void(0)",+ checkmate::assert_multi_class(modules, c("teal_modules", "teal_module", "shiny.tag"))
|
|
| 113 | +41 | ! |
- onclick = sprintf("toggleFilterPanel('%s');", ns("tabpanel_wrapper")),
+ checkmate::assert_count(depth) |
|
| 114 | +42 | ! |
- title = "Toggle filter panel",+ UseMethod("ui_teal_module", modules)
+ |
+ |
| 43 | ++ |
+ }+ |
+ ||
| 44 | ++ | + + | +||
| 45 | ++ |
+ #' @rdname module_teal_module+ |
+ ||
| 46 | ++ |
+ #' @export+ |
+ ||
| 47 | ++ |
+ ui_teal_module.default <- function(id, modules, depth = 0L) {
|
||
| 115 | +48 | ! |
- icon("fas fa-bars")
+ stop("Modules class not supported: ", paste(class(modules), collapse = " "))
|
|
| 116 | +49 |
- ),+ }+ |
+ ||
| 50 | ++ | + + | +||
| 51 | ++ |
+ #' @rdname module_teal_module+ |
+ ||
| 52 | ++ |
+ #' @export+ |
+ ||
| 53 | ++ |
+ ui_teal_module.teal_modules <- function(id, modules, depth = 0L) {
|
||
| 117 | +54 | ! |
- ui_snapshot_manager_panel(ns("snapshot_manager_panel")),
+ ns <- NS(id) |
|
| 118 | +55 | ! |
- ui_filter_manager_panel(ns("filter_manager_panel"))
+ tags$div( |
|
| 119 | -+ | |||
| 56 | +! |
- ),+ id = ns("wrapper"),
|
||
| 120 | +57 | ! |
- tags$script(+ do.call( |
|
| 121 | +58 | ! |
- HTML(+ tabsetPanel, |
|
| 122 | +59 | ! |
- sprintf(+ c( |
|
| 123 | +60 |
- "+ # by giving an id, we can reactively respond to tab changes |
||
| 124 | +61 | ! |
- $(document).ready(function() {
+ list( |
|
| 125 | +62 | ! |
- $('#%s').appendTo('#%s');
+ id = ns("active_tab"),
|
|
| 126 | -+ | |||
| 63 | +! |
- });+ type = if (modules$label == "root") "pills" else "tabs" |
||
| 127 | +64 |
- ",+ ), |
||
| 128 | +65 | ! |
- ns("options_buttons"),
+ lapply( |
|
| 129 | +66 | ! |
- ns("teal_modules-active_tab")
+ names(modules$children), |
|
| 130 | -+ | |||
| 67 | +! |
- )+ function(module_id) {
|
||
| 131 | -+ | |||
| 68 | +! |
- )+ module_label <- modules$children[[module_id]]$label |
||
| 132 | -+ | |||
| 69 | +! |
- ),+ if (is.null(module_label)) {
|
||
| 133 | +70 | ! |
- tags$hr(),+ module_label <- icon("fas fa-database")
+ |
+ |
| 71 | ++ |
+ } |
||
| 134 | +72 | ! |
- tags$footer(+ tabPanel( |
|
| 135 | +73 | ! |
- tags$div(+ title = module_label, |
|
| 136 | +74 | ! |
- footer,+ value = module_id, # when clicked this tab value changes input$<tabset panel id> |
|
| 137 | +75 | ! |
- teal.widgets::verbatim_popup_ui(ns("sessionInfo"), "Session Info", type = "link"),
+ ui_teal_module( |
|
| 138 | +76 | ! |
- br(),+ id = ns(module_id), |
|
| 139 | +77 | ! |
- ui_teal_lockfile(ns("lockfile")),
+ modules = modules$children[[module_id]], |
|
| 140 | +78 | ! |
- textOutput(ns("identifier"))
+ depth = depth + 1L |
|
| 141 | +79 |
- )+ ) |
||
| 142 | +80 |
- )+ ) |
||
| 143 | +81 |
- )+ } |
||
| 144 | +82 |
- }+ ) |
||
| 145 | +83 |
-
+ ) |
||
| 146 | +84 |
- #' @rdname module_teal+ ) |
||
| 147 | +85 |
- #' @export+ ) |
||
| 148 | +86 |
- srv_teal <- function(id, data, modules, filter = teal_slices()) {
- |
- ||
| 149 | -89x | -
- checkmate::assert_character(id, max.len = 1, any.missing = FALSE)+ } |
||
| 150 | -89x | +|||
| 87 | +
- checkmate::assert_multi_class(data, c("teal_data", "teal_data_module", "reactive"))
+
|
|||
| 151 | -88x | +|||
| 88 | +
- checkmate::assert_class(modules, "teal_modules")+ #' @rdname module_teal_module |
|||
| 152 | -88x | +|||
| 89 | +
- checkmate::assert_class(filter, "teal_slices")+ #' @export |
|||
| 153 | +90 |
-
+ ui_teal_module.teal_module <- function(id, modules, depth = 0L) {
|
||
| 154 | -88x | +|||
| 91 | +! |
- moduleServer(id, function(input, output, session) {
+ ns <- NS(id) |
||
| 155 | -88x | +|||
| 92 | +! |
- logger::log_debug("srv_teal initializing.")
+ args <- c(list(id = ns("module")), modules$ui_args)
|
||
| 156 | +93 | |||
| 157 | -88x | +|||
| 94 | +! |
- if (getOption("teal.show_js_log", default = FALSE)) {
+ ui_teal <- tagList( |
||
| 158 | +95 | ! |
- shinyjs::showLog()+ shinyjs::hidden( |
|
| 159 | -+ | |||
| 96 | +! |
- }+ tags$div( |
||
| 160 | -+ | |||
| 97 | +! |
-
+ id = ns("transform_failure_info"),
|
||
| 161 | -88x | +|||
| 98 | +! |
- srv_teal_lockfile("lockfile")
+ class = "teal_validated", |
||
| 162 | -+ | |||
| 99 | +! |
-
+ div( |
||
| 163 | -88x | +|||
| 100 | +! |
- output$identifier <- renderText(+ class = "teal-output-warning", |
||
| 164 | -88x | +|||
| 101 | +! |
- paste0("Pid:", Sys.getpid(), " Token:", substr(session$token, 25, 32))
+ "One of transformators failed. Please check its inputs." |
||
| 165 | +102 |
- )+ ) |
||
| 166 | +103 |
-
+ ) |
||
| 167 | -88x | +|||
| 104 | +
- teal.widgets::verbatim_popup_srv(+ ), |
|||
| 168 | -88x | +|||
| 105 | +! |
- "sessionInfo",+ tags$div( |
||
| 169 | -88x | +|||
| 106 | +! |
- verbatim_content = utils::capture.output(utils::sessionInfo()),+ id = ns("teal_module_ui"),
|
||
| 170 | -88x | +|||
| 107 | +! |
- title = "SessionInfo"+ tags$div( |
||
| 171 | -+ | |||
| 108 | +! |
- )+ class = "teal_validated", |
||
| 172 | -+ | |||
| 109 | +! |
-
+ ui_check_module_datanames(ns("validate_datanames"))
|
||
| 173 | +110 |
- # `JavaScript` code+ ), |
||
| 174 | -88x | +|||
| 111 | +! |
- run_js_files(files = "init.js")+ do.call(modules$ui, args) |
||
| 175 | +112 |
-
+ ) |
||
| 176 | +113 |
- # set timezone in shiny app+ ) |
||
| 177 | +114 |
- # timezone is set in the early beginning so it will be available also+ |
||
| 178 | -+ | |||
| 115 | +! |
- # for `DDL` and all shiny modules+ div( |
||
| 179 | -88x | +|||
| 116 | +! |
- get_client_timezone(session$ns)+ id = id, |
||
| 180 | -88x | +|||
| 117 | +! |
- observeEvent(+ class = "teal_module", |
||
| 181 | -88x | +|||
| 118 | +! |
- eventExpr = input$timezone,+ uiOutput(ns("data_reactive"), inline = TRUE),
|
||
| 182 | -88x | +|||
| 119 | +! |
- once = TRUE,+ tagList( |
||
| 183 | -88x | +|||
| 120 | +! |
- handlerExpr = {
+ if (depth >= 2L) tags$div(style = "mt-6"), |
||
| 184 | +121 | ! |
- session$userData$timezone <- input$timezone+ if (!is.null(modules$datanames)) {
|
|
| 185 | +122 | ! |
- logger::log_debug("srv_teal@1 Timezone set to client's timezone: { input$timezone }.")
+ fluidRow(+ |
+ |
| 123 | +! | +
+ column(width = 9, ui_teal, class = "teal_primary_col"),+ |
+ ||
| 124 | +! | +
+ column(+ |
+ ||
| 125 | +! | +
+ width = 3,+ |
+ ||
| 126 | +! | +
+ ui_data_summary(ns("data_summary")),
+ |
+ ||
| 127 | +! | +
+ ui_filter_data(ns("filter_panel")),
+ |
+ ||
| 128 | +! | +
+ ui_transform_teal_data(ns("data_transform"), transformators = modules$transformators, class = "well"),
+ |
+ ||
| 129 | +! | +
+ class = "teal_secondary_col" |
||
| 186 | +130 |
- }+ ) |
||
| 187 | +131 |
- )+ ) |
||
| 188 | +132 |
-
+ } else {
|
||
| 189 | -88x | +|||
| 133 | +! |
- data_pulled <- srv_init_data("data", data = data)
+ ui_teal |
||
| 190 | +134 |
-
+ } |
||
| 191 | -87x | +|||
| 135 | +
- validate_ui <- tags$div(+ ) |
|||
| 192 | -87x | +|||
| 136 | +
- id = session$ns("validate_messages"),
+ ) |
|||
| 193 | -87x | +|||
| 137 | +
- class = "teal_validated",+ } |
|||
| 194 | -87x | +|||
| 138 | +
- ui_check_class_teal_data(session$ns("class_teal_data")),
+
|
|||
| 195 | -87x | +|||
| 139 | +
- ui_validate_error(session$ns("silent_error")),
+ #' @rdname module_teal_module |
|||
| 196 | -87x | +|||
| 140 | +
- ui_check_module_datanames(session$ns("datanames_warning"))
+ srv_teal_module <- function(id, |
|||
| 197 | +141 |
- )+ data, |
||
| 198 | -87x | +|||
| 142 | +
- srv_check_class_teal_data("class_teal_data", data_pulled)
+ modules, |
|||
| 199 | -87x | +|||
| 143 | +
- srv_validate_error("silent_error", data_pulled, validate_shiny_silent_error = FALSE)
+ datasets = NULL, |
|||
| 200 | -87x | +|||
| 144 | +
- srv_check_module_datanames("datanames_warning", data_pulled, modules)
+ slices_global, |
|||
| 201 | +145 |
-
+ reporter = teal.reporter::Reporter$new(), |
||
| 202 | -87x | +|||
| 146 | +
- data_validated <- .trigger_on_success(data_pulled)+ data_load_status = reactive("ok"),
|
|||
| 203 | +147 |
-
+ is_active = reactive(TRUE)) {
|
||
| 204 | -87x | +148 | +199x |
- data_rv <- reactive({
+ checkmate::assert_string(id) |
| 205 | -152x | +149 | +199x |
- req(inherits(data_validated(), "teal_data"))+ assert_reactive(data) |
| 206 | -75x | +150 | +199x |
- is_filter_ok <- check_filter_datanames(filter, names(data_validated()))+ checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"))
|
| 207 | -75x | +151 | +199x |
- if (!isTRUE(is_filter_ok)) {
+ assert_reactive(datasets, null.ok = TRUE) |
| 208 | -2x | +152 | +199x |
- showNotification(+ checkmate::assert_class(slices_global, ".slicesGlobal") |
| 209 | -2x | +153 | +199x |
- "Some filters were not applied because of incompatibility with data. Contact app developer.",+ checkmate::assert_class(reporter, "Reporter") |
| 210 | -2x | +154 | +199x |
- type = "warning",+ assert_reactive(data_load_status) |
| 211 | -2x | +155 | +199x |
- duration = 10+ UseMethod("srv_teal_module", modules)
|
| 212 | +156 |
- )+ } |
||
| 213 | -2x | +|||
| 157 | +
- warning(is_filter_ok)+ |
|||
| 214 | +158 |
- }+ #' @rdname module_teal_module |
||
| 215 | -75x | +|||
| 159 | +
- .add_signature_to_data(data_validated())+ #' @export |
|||
| 216 | +160 |
- })+ srv_teal_module.default <- function(id, |
||
| 217 | +161 |
-
+ data, |
||
| 218 | -87x | +|||
| 162 | +
- data_load_status <- reactive({
+ modules, |
|||
| 219 | -80x | +|||
| 163 | +
- if (inherits(data_pulled(), "teal_data")) {
+ datasets = NULL, |
|||
| 220 | -75x | +|||
| 164 | +
- "ok"+ slices_global, |
|||
| 221 | -5x | +|||
| 165 | +
- } else if (inherits(data, "teal_data_module")) {
+ reporter = teal.reporter::Reporter$new(), |
|||
| 222 | -5x | +|||
| 166 | +
- "teal_data_module failed"+ data_load_status = reactive("ok"),
|
|||
| 223 | +167 |
- } else {
+ is_active = reactive(TRUE)) {
|
||
| 224 | +168 | ! |
- "external failed"+ stop("Modules class not supported: ", paste(class(modules), collapse = " "))
|
|
| 225 | +169 |
- }+ } |
||
| 226 | +170 |
- })+ |
||
| 227 | +171 | - - | -||
| 228 | -87x | -
- datasets_rv <- if (!isTRUE(attr(filter, "module_specific"))) {
+ #' @rdname module_teal_module |
||
| 229 | -76x | +|||
| 172 | +
- eventReactive(data_rv(), {
+ #' @export |
|||
| 230 | -66x | +|||
| 173 | +
- req(inherits(data_rv(), "teal_data"))+ srv_teal_module.teal_modules <- function(id, |
|||
| 231 | -66x | +|||
| 174 | +
- logger::log_debug("srv_teal@1 initializing FilteredData")
+ data, |
|||
| 232 | -66x | +|||
| 175 | +
- teal_data_to_filtered_data(data_rv())+ modules, |
|||
| 233 | +176 |
- })+ datasets = NULL, |
||
| 234 | +177 |
- }+ slices_global, |
||
| 235 | +178 |
-
+ reporter = teal.reporter::Reporter$new(), |
||
| 236 | +179 |
-
+ data_load_status = reactive("ok"),
|
||
| 237 | +180 |
-
+ is_active = reactive(TRUE)) {
|
||
| 238 | +181 | 87x |
- if (inherits(data, "teal_data_module")) {
+ moduleServer(id = id, module = function(input, output, session) {
|
|
| 239 | -9x | +182 | +87x |
- setBookmarkExclude(c("teal_modules-active_tab"))
+ logger::log_debug("srv_teal_module.teal_modules initializing the module { deparse1(modules$label) }.")
|
| 240 | -9x | +|||
| 183 | +
- shiny::insertTab(+ |
|||
| 241 | -9x | +184 | +87x |
- inputId = "teal_modules-active_tab",+ observeEvent(data_load_status(), {
|
| 242 | -9x | +185 | +80x |
- position = "before",+ tabs_selector <- sprintf("#%s li a", session$ns("active_tab"))
|
| 243 | -9x | +186 | +80x |
- select = TRUE,+ if (identical(data_load_status(), "ok")) {
|
| 244 | -9x | +187 | +75x |
- tabPanel(+ logger::log_debug("srv_teal_module@1 enabling modules tabs.")
|
| 245 | -9x | +188 | +75x |
- title = icon("fas fa-database"),
+ shinyjs::show("wrapper")
|
| 246 | -9x | +189 | +75x |
- value = "teal_data_module",+ shinyjs::enable(selector = tabs_selector) |
| 247 | -9x | +190 | +5x |
- tags$div(+ } else if (identical(data_load_status(), "teal_data_module failed")) {
|
| 248 | -9x | -
- ui_init_data(session$ns("data")),
- |
- ||
| 249 | -9x | -
- validate_ui- |
- ||
| 250 | -- |
- )- |
- ||
| 251 | -- |
- )- |
- ||
| 252 | -- |
- )- |
- ||
| 253 | -- | - - | -||
| 254 | -9x | -
- if (attr(data, "once")) {
- |
- ||
| 255 | -9x | +191 | +5x |
- observeEvent(data_rv(), once = TRUE, {
+ logger::log_debug("srv_teal_module@1 disabling modules tabs.")
|
| 256 | -4x | +192 | +5x |
- logger::log_debug("srv_teal@2 removing data tab.")
+ shinyjs::disable(selector = tabs_selector) |
| 257 | -+ | |||
| 193 | +! |
- # when once = TRUE we pull data once and then remove data tab+ } else if (identical(data_load_status(), "external failed")) {
|
||
| 258 | -4x | +|||
| 194 | +! |
- removeTab("teal_modules-active_tab", target = "teal_data_module")
+ logger::log_debug("srv_teal_module@1 hiding modules tabs.")
|
||
| 259 | -+ | |||
| 195 | +! |
- })+ shinyjs::hide("wrapper")
|
||
| 260 | +196 |
} |
||
| 261 | +197 |
- } else {
+ }) |
||
| 262 | +198 |
- # when no teal_data_module then we want to display messages above tabsetPanel (because there is no data-tab)+ |
||
| 263 | -78x | +199 | +87x |
- insertUI(+ modules_output <- sapply( |
| 264 | -78x | +200 | +87x |
- selector = sprintf("#%s", session$ns("tabpanel_wrapper")),
+ names(modules$children), |
| 265 | -78x | +201 | +87x |
- where = "beforeBegin",+ function(module_id) {
|
| 266 | -78x | -
- ui = tags$div(validate_ui, tags$br())- |
- ||
| 267 | -- |
- )- |
- ||
| 268 | -+ | 202 | +112x |
- }+ srv_teal_module( |
| 269 | -+ | |||
| 203 | +112x |
-
+ id = module_id, |
||
| 270 | -87x | +204 | +112x |
- module_labels <- unlist(module_labels(modules), use.names = FALSE)+ data = data, |
| 271 | -87x | +205 | +112x |
- slices_global <- methods::new(".slicesGlobal", filter, module_labels)
+ modules = modules$children[[module_id]], |
| 272 | -87x | +206 | +112x |
- modules_output <- srv_teal_module(+ datasets = datasets, |
| 273 | -87x | +207 | +112x |
- id = "teal_modules",+ slices_global = slices_global, |
| 274 | -87x | +208 | +112x |
- data_rv = data_rv,+ reporter = reporter, |
| 275 | -87x | +209 | +112x |
- datasets = datasets_rv,+ is_active = reactive( |
| 276 | -87x | +210 | +112x |
- modules = modules,+ is_active() && |
| 277 | -87x | +211 | +112x |
- slices_global = slices_global,+ input$active_tab == module_id && |
| 278 | -87x | +212 | +112x |
- data_load_status = data_load_status+ identical(data_load_status(), "ok") |
| 279 | +213 |
- )+ ) |
||
| 280 | -87x | +|||
| 214 | +
- mapping_table <- srv_filter_manager_panel("filter_manager_panel", slices_global = slices_global)
+ ) |
|||
| 281 | -87x | +|||
| 215 | +
- snapshots <- srv_snapshot_manager_panel("snapshot_manager_panel", slices_global = slices_global)
+ }, |
|||
| 282 | +216 | 87x |
- srv_bookmark_panel("bookmark_manager", modules)
+ simplify = FALSE |
|
| 283 | +217 |
- })+ ) |
||
| 284 | +218 | |||
| 285 | +219 | 87x |
- invisible(NULL)+ modules_output |
|
| 286 | +220 |
- }+ }) |
| 1 | +221 |
- #' Get client timezone+ } |
||
| 2 | +222 |
- #'+ |
||
| 3 | +223 |
- #' User timezone in the browser may be different to the one on the server.+ #' @rdname module_teal_module |
||
| 4 | +224 |
- #' This script can be run to register a `shiny` input which contains information about the timezone in the browser.+ #' @export |
||
| 5 | +225 |
- #'+ srv_teal_module.teal_module <- function(id, |
||
| 6 | +226 |
- #' @param ns (`function`) namespace function passed from the `session` object in the `shiny` server.+ data, |
||
| 7 | +227 |
- #' For `shiny` modules this will allow for proper name spacing of the registered input.+ modules, |
||
| 8 | +228 |
- #'+ datasets = NULL, |
||
| 9 | +229 |
- #' @return `NULL`, invisibly.+ slices_global, |
||
| 10 | +230 |
- #'+ reporter = teal.reporter::Reporter$new(), |
||
| 11 | +231 |
- #' @keywords internal+ data_load_status = reactive("ok"),
|
||
| 12 | +232 |
- #'+ is_active = reactive(TRUE)) {
|
||
| 13 | -+ | |||
| 233 | +112x |
- get_client_timezone <- function(ns) {
+ logger::log_debug("srv_teal_module.teal_module initializing the module: { deparse1(modules$label) }.")
|
||
| 14 | -88x | +234 | +112x |
- script <- sprintf(+ moduleServer(id = id, module = function(input, output, session) {
|
| 15 | -88x | +235 | +112x |
- "Shiny.setInputValue(`%s`, Intl.DateTimeFormat().resolvedOptions().timeZone)",+ module_out <- reactiveVal()+ |
+
| 236 | ++ | + | ||
| 16 | -88x | +237 | +112x |
- ns("timezone")
+ active_datanames <- reactive({
+ |
+
| 238 | +89x | +
+ .resolve_module_datanames(data = data(), modules = modules) |
||
| 17 | +239 |
- )+ }) |
||
| 18 | -88x | +240 | +112x |
- shinyjs::runjs(script) # function does not return anything+ if (is.null(datasets)) {
|
| 19 | -88x | +241 | +20x |
- invisible(NULL)+ datasets <- eventReactive(data(), {
|
| 20 | -+ | |||
| 242 | +16x |
- }+ req(inherits(data(), "teal_data")) |
||
| 21 | -+ | |||
| 243 | +16x |
-
+ logger::log_debug("srv_teal_module@1 initializing module-specific FilteredData")
|
||
| 22 | -+ | |||
| 244 | +16x |
- #' Resolve the expected bootstrap theme+ teal_data_to_filtered_data(data(), datanames = active_datanames()) |
||
| 23 | +245 |
- #' @noRd+ }) |
||
| 24 | +246 |
- #' @keywords internal+ } |
||
| 25 | +247 |
- get_teal_bs_theme <- function() {
+
|
||
| 26 | -4x | +|||
| 248 | +
- bs_theme <- getOption("teal.bs_theme")
+ # manage module filters on the module level |
|||
| 27 | +249 |
-
+ # important: |
||
| 28 | -4x | +|||
| 250 | +
- if (is.null(bs_theme)) {
+ # filter_manager_module_srv needs to be called before filter_panel_srv |
|||
| 29 | -1x | +|||
| 251 | +
- return(NULL)+ # Because available_teal_slices is used in FilteredData$srv_available_slices (via srv_filter_panel) |
|||
| 30 | +252 |
- }+ # and if it is not set, then it won't be available in the srv_filter_panel+ |
+ ||
| 253 | +112x | +
+ srv_module_filter_manager(modules$label, module_fd = datasets, slices_global = slices_global) |
||
| 31 | +254 | |||
| 32 | -3x | +255 | +112x |
- if (!checkmate::test_class(bs_theme, "bs_theme")) {
+ call_once_when(is_active(), {
|
| 33 | -2x | +256 | +86x |
- warning(+ filtered_teal_data <- srv_filter_data( |
| 34 | -2x | +257 | +86x |
- "Assertion on 'teal.bs_theme' option value failed: ",+ "filter_panel", |
| 35 | -2x | +258 | +86x |
- checkmate::check_class(bs_theme, "bs_theme"),+ datasets = datasets, |
| 36 | -2x | +259 | +86x |
- ". The default Shiny Bootstrap theme will be used."+ active_datanames = active_datanames, |
| 37 | -+ | |||
| 260 | +86x |
- )+ data = data, |
||
| 38 | -2x | +261 | +86x |
- return(NULL)+ is_active = is_active |
| 39 | +262 |
- }+ ) |
||
| 40 | -+ | |||
| 263 | +86x |
-
+ is_transform_failed <- reactiveValues() |
||
| 41 | -1x | +264 | +86x |
- bs_theme+ transformed_teal_data <- srv_transform_teal_data( |
| 42 | -+ | |||
| 265 | +86x |
- }+ "data_transform", |
||
| 43 | -+ | |||
| 266 | +86x |
-
+ data = filtered_teal_data, |
||
| 44 | -+ | |||
| 267 | +86x |
- #' Return parentnames along with datanames.+ transformators = modules$transformators, |
||
| 45 | -+ | |||
| 268 | +86x |
- #' @noRd+ modules = modules, |
||
| 46 | -+ | |||
| 269 | +86x |
- #' @keywords internal+ is_transform_failed = is_transform_failed |
||
| 47 | +270 |
- .include_parent_datanames <- function(datanames, join_keys) {
+ ) |
||
| 48 | -32x | +271 | +86x |
- ordered_datanames <- datanames+ any_transform_failed <- reactive({
|
| 49 | -32x | +272 | +86x |
- for (current in datanames) {
+ any(unlist(reactiveValuesToList(is_transform_failed)))+ |
+
| 273 | ++ |
+ })+ |
+ ||
| 274 | ++ | + | ||
| 50 | -62x | +275 | +86x |
- parents <- character(0L)+ observeEvent(any_transform_failed(), {
|
| 51 | -62x | +276 | +86x |
- while (length(current) > 0) {
+ if (isTRUE(any_transform_failed())) {
|
| 52 | -64x | +277 | +6x |
- current <- teal.data::parent(join_keys, current)+ shinyjs::hide("teal_module_ui")
|
| 53 | -64x | +278 | +6x |
- parents <- c(current, parents)+ shinyjs::show("transform_failure_info")
|
| 54 | +279 |
- }+ } else {
|
||
| 55 | -62x | +280 | +80x |
- ordered_datanames <- c(parents, ordered_datanames)+ shinyjs::show("teal_module_ui")
+ |
+
| 281 | +80x | +
+ shinyjs::hide("transform_failure_info")
|
||
| 56 | +282 |
- }+ } |
||
| 57 | +283 | ++ |
+ })+ |
+ |
| 284 | ||||
| 58 | -32x | +285 | +86x |
- unique(ordered_datanames)+ module_teal_data <- reactive({
|
| 59 | -+ | |||
| 286 | +94x |
- }+ req(inherits(transformed_teal_data(), "teal_data")) |
||
| 60 | -+ | |||
| 287 | +88x |
-
+ all_teal_data <- transformed_teal_data() |
||
| 61 | -+ | |||
| 288 | +88x |
- #' Create a `FilteredData`+ module_datanames <- .resolve_module_datanames(data = all_teal_data, modules = modules) |
||
| 62 | -+ | |||
| 289 | +88x |
- #'+ all_teal_data[c(module_datanames, ".raw_data")] |
||
| 63 | +290 |
- #' Create a `FilteredData` object from a `teal_data` object.+ }) |
||
| 64 | +291 |
- #'+ |
||
| 65 | -+ | |||
| 292 | +86x |
- #' @param x (`teal_data`) object+ srv_check_module_datanames( |
||
| 66 | -+ | |||
| 293 | +86x |
- #' @param datanames (`character`) vector of data set names to include; must be subset of `names(x)`+ "validate_datanames", |
||
| 67 | -+ | |||
| 294 | +86x |
- #' @return A `FilteredData` object.+ data = module_teal_data,+ |
+ ||
| 295 | +86x | +
+ modules = modules |
||
| 68 | +296 |
- #' @keywords internal+ ) |
||
| 69 | +297 |
- teal_data_to_filtered_data <- function(x, datanames = names(x)) {
+
|
||
| 70 | -83x | +298 | +86x |
- checkmate::assert_class(x, "teal_data")+ summary_table <- srv_data_summary("data_summary", module_teal_data)
|
| 71 | -83x | +|||
| 299 | +
- checkmate::assert_character(datanames, min.chars = 1L, any.missing = FALSE)+ |
|||
| 72 | +300 |
- # Otherwise, FilteredData will be created in the modules' scope later+ # Call modules. |
||
| 73 | -83x | +301 | +86x |
- teal.slice::init_filtered_data(+ if (!inherits(modules, "teal_module_previewer")) {
|
| 74 | -83x | +302 | +86x |
- x = Filter(length, sapply(datanames, function(dn) x[[dn]], simplify = FALSE)),+ obs_module <- call_once_when( |
| 75 | -83x | +303 | +86x |
- join_keys = teal.data::join_keys(x)+ !is.null(module_teal_data()), |
| 76 | -+ | |||
| 304 | +86x |
- )+ ignoreNULL = TRUE, |
||
| 77 | -+ | |||
| 305 | +86x |
- }+ handlerExpr = {
|
||
| 78 | -+ | |||
| 306 | +80x |
-
+ module_out(.call_teal_module(modules, datasets, module_teal_data, reporter)) |
||
| 79 | +307 |
-
+ } |
||
| 80 | +308 |
- #' Template function for `TealReportCard` creation and customization+ ) |
||
| 81 | +309 |
- #'+ } else {
|
||
| 82 | +310 |
- #' This function generates a report card with a title,+ # Report previewer must be initiated on app start for report cards to be included in bookmarks. |
||
| 83 | +311 |
- #' an optional description, and the option to append the filter state list.+ # When previewer is delayed, cards are bookmarked only if previewer has been initiated (visited). |
||
| 84 | -+ | |||
| 312 | +! |
- #'+ module_out(.call_teal_module(modules, datasets, module_teal_data, reporter)) |
||
| 85 | +313 |
- #' @param title (`character(1)`) title of the card (unless overwritten by label)+ } |
||
| 86 | +314 |
- #' @param label (`character(1)`) label provided by the user when adding the card+ }) |
||
| 87 | +315 |
- #' @param description (`character(1)`) optional, additional description+ |
||
| 88 | -+ | |||
| 316 | +112x |
- #' @param with_filter (`logical(1)`) flag indicating to add filter state+ module_out |
||
| 89 | +317 |
- #' @param filter_panel_api (`FilterPanelAPI`) object with API that allows the generation+ }) |
||
| 90 | +318 |
- #' of the filter state in the report+ } |
||
| 91 | +319 |
- #'+ |
||
| 92 | +320 |
- #' @return (`TealReportCard`) populated with a title, description and filter state.+ # This function calls a module server function. |
||
| 93 | +321 |
- #'+ .call_teal_module <- function(modules, datasets, data, reporter) {
|
||
| 94 | -+ | |||
| 322 | +80x |
- #' @export+ assert_reactive(data) |
||
| 95 | +323 |
- report_card_template <- function(title, label, description = NULL, with_filter, filter_panel_api) {
+
|
||
| 96 | -2x | +|||
| 324 | +
- checkmate::assert_string(title)+ # collect arguments to run teal_module |
|||
| 97 | -2x | +325 | +80x |
- checkmate::assert_string(label)+ args <- c(list(id = "module"), modules$server_args) |
| 98 | -2x | +326 | +80x |
- checkmate::assert_string(description, null.ok = TRUE)+ if (is_arg_used(modules$server, "reporter")) {
|
| 99 | -2x | +327 | +1x |
- checkmate::assert_flag(with_filter)+ args <- c(args, list(reporter = reporter)) |
| 100 | -2x | +|||
| 328 | +
- checkmate::assert_class(filter_panel_api, classes = "FilterPanelAPI")+ } |
|||
| 101 | +329 | |||
| 102 | -2x | +330 | +80x |
- card <- teal::TealReportCard$new()+ if (is_arg_used(modules$server, "datasets")) {
|
| 103 | -2x | +331 | +1x |
- title <- if (label == "") title else label+ args <- c(args, datasets = datasets()) |
| 104 | -2x | +332 | +1x |
- card$set_name(title)+ warning("datasets argument is not reactive and therefore it won't be updated when data is refreshed.")
|
| 105 | -2x | +|||
| 333 | +
- card$append_text(title, "header2")+ } |
|||
| 106 | -1x | +|||
| 334 | +
- if (!is.null(description)) card$append_text(description, "header3")+ |
|||
| 107 | -1x | +335 | +80x |
- if (with_filter) card$append_fs(filter_panel_api$get_filter_state())+ if (is_arg_used(modules$server, "data")) {
|
| 108 | -2x | +336 | +76x |
- card+ args <- c(args, data = list(data)) |
| 109 | +337 |
- }+ } |
||
| 110 | +338 | |||
| 111 | -+ | |||
| 339 | +80x |
-
+ if (is_arg_used(modules$server, "filter_panel_api")) {
|
||
| 112 | -+ | |||
| 340 | +1x |
- #' Check `datanames` in modules+ args <- c(args, filter_panel_api = teal.slice::FilterPanelAPI$new(datasets())) |
||
| 113 | +341 |
- #'+ } |
||
| 114 | +342 |
- #' These functions check if specified `datanames` in modules match those in the data object,+ |
||
| 115 | -+ | |||
| 343 | +80x |
- #' returning error messages or `TRUE` for successful validation. Two functions return error message+ if (is_arg_used(modules$server, "id")) {
|
||
| 116 | -+ | |||
| 344 | +80x |
- #' in different forms:+ do.call(modules$server, args) |
||
| 117 | +345 |
- #' - `check_modules_datanames` returns `character(1)` for basic assertion usage+ } else {
|
||
| 118 | -+ | |||
| 346 | +! |
- #' - `check_modules_datanames_html` returns `shiny.tag.list` to display it in the app.+ do.call(callModule, c(args, list(module = modules$server))) |
||
| 119 | +347 |
- #'+ } |
||
| 120 | +348 |
- #' @param modules (`teal_modules`) object+ } |
||
| 121 | +349 |
- #' @param datanames (`character`) names of datasets available in the `data` object+ |
||
| 122 | +350 |
- #'+ .resolve_module_datanames <- function(data, modules) {
|
||
| 123 | -+ | |||
| 351 | +177x |
- #' @return `TRUE` if validation passes, otherwise `character(1)` or `shiny.tag.list`+ stopifnot("data must be teal_data object." = inherits(data, "teal_data"))
|
||
| 124 | -+ | |||
| 352 | +177x |
- #' @keywords internal+ if (is.null(modules$datanames) || identical(modules$datanames, "all")) {
|
||
| 125 | -+ | |||
| 353 | +145x |
- check_modules_datanames <- function(modules, datanames) {
+ names(data) |
||
| 126 | -11x | +|||
| 354 | +
- out <- check_modules_datanames_html(modules, datanames)+ } else {
|
|||
| 127 | -11x | +355 | +32x |
- if (inherits(out, "shiny.tag.list")) {
+ intersect( |
| 128 | -5x | +356 | +32x |
- out_with_ticks <- gsub("<code>|</code>", "`", toString(out))
+ names(data), # Keep topological order from teal.data::names() |
| 129 | -5x | +357 | +32x |
- out_text <- gsub("<[^<>]+>", "", toString(out_with_ticks))
- |
-
| 130 | -5x | -
- trimws(gsub("[[:space:]]+", " ", out_text))
+ .include_parent_datanames(modules$datanames, teal.data::join_keys(data)) |
||
| 131 | +358 |
- } else {
- |
- ||
| 132 | -6x | -
- out+ ) |
||
| 133 | +359 |
} |
||
| 134 | +360 |
} |
||
| 135 | +361 | |||
| 136 | +362 |
- #' @rdname check_modules_datanames+ #' Calls expression when condition is met |
||
| 137 | +363 |
- check_reserved_datanames <- function(datanames) {
- |
- ||
| 138 | -190x | -
- reserved_datanames <- datanames[datanames %in% c("all", ".raw_data")]
- |
- ||
| 139 | -190x | -
- if (length(reserved_datanames) == 0L) {
+ #' |
||
| 140 | -184x | +|||
| 364 | +
- return(NULL)+ #' Function postpones `handlerExpr` to the moment when `eventExpr` (condition) returns `TRUE`, |
|||
| 141 | +365 |
- }+ #' otherwise nothing happens. |
||
| 142 | +366 |
-
+ #' @param eventExpr A (quoted or unquoted) logical expression that represents the event; |
||
| 143 | -6x | +|||
| 367 | +
- tags$span(+ #' this can be a simple reactive value like input$click, a call to a reactive expression |
|||
| 144 | -6x | +|||
| 368 | +
- to_html_code_list(reserved_datanames),+ #' like dataset(), or even a complex expression inside curly braces. |
|||
| 145 | -6x | +|||
| 369 | +
- sprintf(+ #' @param ... additional arguments passed to `observeEvent` with the exception of `eventExpr` that is not allowed. |
|||
| 146 | -6x | +|||
| 370 | +
- "%s reserved for internal use. Please avoid using %s as %s.",+ #' @inheritParams shiny::observeEvent |
|||
| 147 | -6x | +|||
| 371 | +
- pluralize(reserved_datanames, "is", "are"),+ #' |
|||
| 148 | -6x | +|||
| 372 | +
- pluralize(reserved_datanames, "it", "them"),+ #' @return An observer. |
|||
| 149 | -6x | +|||
| 373 | +
- pluralize(reserved_datanames, "a dataset name", "dataset names")+ #' |
|||
| 150 | +374 |
- )+ #' @keywords internal |
||
| 151 | +375 |
- )+ call_once_when <- function(eventExpr, # nolint: object_name. |
||
| 152 | +376 |
- }+ handlerExpr, # nolint: object_name. |
||
| 153 | +377 |
-
+ event.env = parent.frame(), # nolint: object_name. |
||
| 154 | +378 |
- #' @rdname check_modules_datanames+ handler.env = parent.frame(), # nolint: object_name. |
||
| 155 | +379 |
- check_modules_datanames_html <- function(modules, datanames) {
+ ...) {
|
||
| 156 | -190x | +380 | +198x |
- check_datanames <- check_modules_datanames_recursive(modules, datanames)+ event_quo <- rlang::new_quosure(substitute(eventExpr), env = event.env) |
| 157 | -190x | +381 | +198x |
- show_module_info <- inherits(modules, "teal_modules") # used in two contexts - module and app+ handler_quo <- rlang::new_quosure(substitute(handlerExpr), env = handler.env) |
| 158 | +382 | |||
| 159 | -190x | -
- reserved_datanames <- check_reserved_datanames(datanames)- |
- ||
| 160 | +383 |
-
+ # When `condExpr` is TRUE, then `handlerExpr` is evaluated once. |
||
| 161 | -190x | +384 | +198x |
- if (!length(check_datanames)) {
+ activator <- reactive({
|
| 162 | -172x | +385 | +198x |
- out <- if (is.null(reserved_datanames)) {
+ if (isTRUE(rlang::eval_tidy(event_quo))) {
|
| 163 | +386 | 166x |
TRUE |
|
| 164 | +387 |
- } else {
- |
- ||
| 165 | -6x | -
- shiny::tagList(reserved_datanames)+ } |
||
| 166 | +388 |
- }- |
- ||
| 167 | -172x | -
- return(out)+ }) |
||
| 168 | +389 |
- }+ |
||
| 169 | -18x | +390 | +198x |
- shiny::tagList(+ observeEvent( |
| 170 | -18x | +391 | +198x |
- reserved_datanames,+ eventExpr = activator(), |
| 171 | -18x | +392 | +198x |
- lapply(+ once = TRUE, |
| 172 | -18x | +393 | +198x |
- check_datanames,+ handlerExpr = rlang::eval_tidy(handler_quo), |
| 173 | -18x | +|||
| 394 | +
- function(mod) {
+ ... |
|||
| 174 | -18x | +|||
| 395 | +
- tagList(+ ) |
|||
| 175 | -18x | +|||
| 396 | +
- tags$span(+ } |
|||
| 176 | -18x | +
| 1 | +
- tags$span(pluralize(mod$missing_datanames, "Dataset")),+ #' Filter state snapshot management |
|||
| 177 | -18x | +|||
| 2 | +
- to_html_code_list(mod$missing_datanames),+ #' |
|||
| 178 | -18x | +|||
| 3 | +
- tags$span(+ #' Capture and restore snapshots of the global (app) filter state. |
|||
| 179 | -18x | +|||
| 4 | +
- sprintf(+ #' |
|||
| 180 | -18x | +|||
| 5 | +
- "%s missing%s.",+ #' This module introduces snapshots: stored descriptions of the filter state of the entire application. |
|||
| 181 | -18x | +|||
| 6 | +
- pluralize(mod$missing_datanames, "is", "are"),+ #' Snapshots allow the user to save the current filter state of the application for later use in the session, |
|||
| 182 | -18x | +|||
| 7 | +
- if (show_module_info) sprintf(" for module '%s'", mod$label) else ""
+ #' as well as to save it to file in order to share it with an app developer or other users, |
|||
| 183 | +8 |
- )+ #' who in turn can upload it to their own session. |
||
| 184 | +9 |
- )+ #' |
||
| 185 | +10 |
- ),+ #' The snapshot manager is accessed with the camera icon in the tabset bar. |
||
| 186 | -18x | +|||
| 11 | +
- if (length(datanames) >= 1) {
+ #' At the beginning of a session it presents three icons: a camera, an upload, and an circular arrow. |
|||
| 187 | -16x | +|||
| 12 | +
- tagList(+ #' Clicking the camera captures a snapshot, clicking the upload adds a snapshot from a file |
|||
| 188 | -16x | +|||
| 13 | +
- tags$span(pluralize(datanames, "Dataset")),+ #' and applies the filter states therein, and clicking the arrow resets initial application state. |
|||
| 189 | -16x | +|||
| 14 | +
- tags$span("available in data:"),
+ #' As snapshots are added, they will show up as rows in a table and each will have a select button and a save button. |
|||
| 190 | -16x | +|||
| 15 | +
- tagList(+ #' |
|||
| 191 | -16x | +|||
| 16 | +
- tags$span(+ #' @section Server logic: |
|||
| 192 | -16x | +|||
| 17 | +
- to_html_code_list(datanames),+ #' Snapshots are basically `teal_slices` objects, however, since each module is served by a separate instance |
|||
| 193 | -16x | +|||
| 18 | +
- tags$span(".", .noWS = "outside"),
+ #' of `FilteredData` and these objects require shared state, `teal_slice` is a `reactiveVal` so `teal_slices` |
|||
| 194 | -16x | +|||
| 19 | +
- .noWS = c("outside")
+ #' cannot be stored as is. Therefore, `teal_slices` are reversibly converted to a list of lists representation |
|||
| 195 | +20 |
- )+ #' (attributes are maintained). |
||
| 196 | +21 |
- )+ #' |
||
| 197 | +22 |
- )+ #' Snapshots are stored in a `reactiveVal` as a named list. |
||
| 198 | +23 |
- } else {
+ #' The first snapshot is the initial state of the application and the user can add a snapshot whenever they see fit. |
||
| 199 | -2x | +|||
| 24 | +
- tags$span("No datasets are available in data.")
+ #' |
|||
| 200 | +25 |
- },+ #' For every snapshot except the initial one, a piece of UI is generated that contains |
||
| 201 | -18x | +|||
| 26 | +
- tags$br(.noWS = "before")+ #' the snapshot name, a select button to restore that snapshot, and a save button to save it to a file. |
|||
| 202 | +27 |
- )+ #' The initial snapshot is restored by a separate "reset" button. |
||
| 203 | +28 |
- }+ #' It cannot be saved directly but a user is welcome to capture the initial state as a snapshot and save that. |
||
| 204 | +29 |
- )+ #' |
||
| 205 | +30 |
- )+ #' @section Snapshot mechanics: |
||
| 206 | +31 |
- }+ #' When a snapshot is captured, the user is prompted to name it. |
||
| 207 | +32 |
-
+ #' Names are displayed as is but since they are used to create button ids, |
||
| 208 | +33 |
- #' Recursively checks modules and returns list for every datanames mismatch between module and data+ #' under the hood they are converted to syntactically valid strings. |
||
| 209 | +34 |
- #' @noRd+ #' New snapshot names are validated so that their valid versions are unique. |
||
| 210 | +35 |
- check_modules_datanames_recursive <- function(modules, datanames) { # nolint: object_name_length
+ #' Leading and trailing white space is trimmed. |
||
| 211 | -296x | +|||
| 36 | +
- checkmate::assert_multi_class(modules, c("teal_module", "teal_modules"))
+ #' |
|||
| 212 | -296x | +|||
| 37 | +
- checkmate::assert_character(datanames)+ #' The module can read the global state of the application from `slices_global` and `mapping_matrix`. |
|||
| 213 | -296x | +|||
| 38 | +
- if (inherits(modules, "teal_modules")) {
+ #' The former provides a list of all existing `teal_slice`s and the latter says which slice is active in which module. |
|||
| 214 | -86x | +|||
| 39 | +
- unlist(+ #' Once a name has been accepted, `slices_global` is converted to a list of lists - a snapshot. |
|||
| 215 | -86x | +|||
| 40 | +
- lapply(modules$children, check_modules_datanames_recursive, datanames = datanames),+ #' The snapshot contains the `mapping` attribute of the initial application state |
|||
| 216 | -86x | +|||
| 41 | +
- recursive = FALSE+ #' (or one that has been restored), which may not reflect the current one, |
|||
| 217 | +42 |
- )+ #' so `mapping_matrix` is transformed to obtain the current mapping, i.e. a list that, |
||
| 218 | +43 |
- } else {
+ #' when passed to the `mapping` argument of [teal_slices()], would result in the current mapping. |
||
| 219 | -210x | +|||
| 44 | +
- missing_datanames <- setdiff(modules$datanames, c("all", datanames))
+ #' This is substituted as the snapshot's `mapping` attribute and the snapshot is added to the snapshot list. |
|||
| 220 | -210x | +|||
| 45 | +
- if (length(missing_datanames)) {
+ #' |
|||
| 221 | -18x | +|||
| 46 | +
- list(list(+ #' To restore app state, a snapshot is retrieved from storage and rebuilt into a `teal_slices` object. |
|||
| 222 | -18x | +|||
| 47 | +
- label = modules$label,+ #' Then state of all `FilteredData` objects (provided in `datasets`) is cleared |
|||
| 223 | -18x | +|||
| 48 | +
- missing_datanames = missing_datanames+ #' and set anew according to the `mapping` attribute of the snapshot. |
|||
| 224 | +49 |
- ))+ #' The snapshot is then set as the current content of `slices_global`. |
||
| 225 | +50 |
- }+ #' |
||
| 226 | +51 |
- }+ #' To save a snapshot, the snapshot is retrieved and reassembled just like for restoring, |
||
| 227 | +52 |
- }+ #' and then saved to file with [slices_store()]. |
||
| 228 | +53 |
-
+ #' |
||
| 229 | +54 |
- #' Convert character vector to html code separated with commas and "and"+ #' When a snapshot is uploaded, it will first be added to storage just like a newly created one, |
||
| 230 | +55 |
- #' @noRd+ #' and then used to restore app state much like a snapshot taken from storage. |
||
| 231 | +56 |
- to_html_code_list <- function(x) {
+ #' Upon clicking the upload icon the user will be prompted for a file to upload |
||
| 232 | -40x | +|||
| 57 | +
- checkmate::assert_character(x)+ #' and may choose to name the new snapshot. The name defaults to the name of the file (the extension is dropped) |
|||
| 233 | -40x | +|||
| 58 | +
- do.call(+ #' and normal naming rules apply. Loading the file yields a `teal_slices` object, |
|||
| 234 | -40x | +|||
| 59 | +
- tagList,+ #' which is disassembled for storage and used directly for restoring app state. |
|||
| 235 | -40x | +|||
| 60 | +
- lapply(seq_along(x), function(.ix) {
+ #' |
|||
| 236 | -56x | +|||
| 61 | +
- tagList(+ #' @section Transferring snapshots: |
|||
| 237 | -56x | +|||
| 62 | +
- tags$code(x[.ix]),+ #' Snapshots uploaded from disk should only be used in the same application they come from, |
|||
| 238 | -56x | +|||
| 63 | +
- if (.ix != length(x)) {
+ #' _i.e._ an application that uses the same data and the same modules. |
|||
| 239 | -1x | +|||
| 64 | +
- if (.ix == length(x) - 1) tags$span(" and ") else tags$span(", ", .noWS = "before")
+ #' To ensure this is the case, `init` stamps `teal_slices` with an app id that is stored in the `app_id` attribute of |
|||
| 240 | +65 |
- }+ #' a `teal_slices` object. When a snapshot is restored from file, its `app_id` is compared to that |
||
| 241 | +66 |
- )+ #' of the current app state and only if the match is the snapshot admitted to the session. |
||
| 242 | +67 |
- })+ #' |
||
| 243 | +68 |
- )+ #' @section Bookmarks: |
||
| 244 | +69 |
- }+ #' An `onBookmark` callback creates a snapshot of the current filter state. |
||
| 245 | +70 |
-
+ #' This is done on the app session, not the module session. |
||
| 246 | +71 |
-
+ #' (The snapshot will be retrieved by `module_teal` in order to set initial app state in a restored app.) |
||
| 247 | +72 |
- #' Check `datanames` in filters+ #' Then that snapshot, and the previous snapshot history are dumped into the `values.rds` file in `<bookmark_dir>`. |
||
| 248 | +73 |
#' |
||
| 249 | +74 |
- #' This function checks whether `datanames` in filters correspond to those in `data`,+ #' @param id (`character(1)`) `shiny` module instance id. |
||
| 250 | +75 |
- #' returning character vector with error messages or `TRUE` if all checks pass.+ #' @param slices_global (`reactiveVal`) that contains a `teal_slices` object |
||
| 251 | +76 |
- #'+ #' containing all `teal_slice`s existing in the app, both active and inactive. |
||
| 252 | +77 |
- #' @param filters (`teal_slices`) object+ #' |
||
| 253 | +78 |
- #' @param datanames (`character`) names of datasets available in the `data` object+ #' @return `list` containing the snapshot history, where each element is an unlisted `teal_slices` object. |
||
| 254 | +79 |
#' |
||
| 255 | +80 |
- #' @return A `character(1)` containing error message or TRUE if validation passes.+ #' @name module_snapshot_manager |
||
| 256 | +81 |
- #' @keywords internal+ #' @rdname module_snapshot_manager |
||
| 257 | +82 |
- check_filter_datanames <- function(filters, datanames) {
+ #' |
||
| 258 | -86x | +|||
| 83 | +
- checkmate::assert_class(filters, "teal_slices")+ #' @author Aleksander Chlebowski |
|||
| 259 | -86x | +|||
| 84 | +
- checkmate::assert_character(datanames)+ #' @keywords internal |
|||
| 260 | +85 |
-
+ NULL |
||
| 261 | +86 |
- # check teal_slices against datanames+ |
||
| 262 | -86x | +|||
| 87 | +
- out <- unlist(sapply(+ #' @rdname module_snapshot_manager |
|||
| 263 | -86x | +|||
| 88 | +
- filters, function(filter) {
+ ui_snapshot_manager_panel <- function(id) {
|
|||
| 264 | -24x | +|||
| 89 | +! |
- dataname <- shiny::isolate(filter$dataname)+ ns <- NS(id) |
||
| 265 | -24x | +|||
| 90 | +! |
- if (!dataname %in% datanames) {
+ tags$button( |
||
| 266 | -3x | +|||
| 91 | +! |
- sprintf(+ id = ns("show_snapshot_manager"),
|
||
| 267 | -3x | +|||
| 92 | +! |
- "- Filter '%s' refers to dataname not available in 'data':\n %s not in (%s)",+ class = "btn action-button wunder_bar_button", |
||
| 268 | -3x | +|||
| 93 | +! |
- shiny::isolate(filter$id),+ title = "View filter mapping", |
||
| 269 | -3x | +|||
| 94 | +! |
- dQuote(dataname, q = FALSE),+ suppressMessages(icon("fas fa-camera"))
|
||
| 270 | -3x | +|||
| 95 | +
- toString(dQuote(datanames, q = FALSE))+ ) |
|||
| 271 | +96 |
- )+ } |
||
| 272 | +97 |
- }+ |
||
| 273 | +98 |
- }+ #' @rdname module_snapshot_manager |
||
| 274 | +99 |
- ))+ srv_snapshot_manager_panel <- function(id, slices_global) {
|
||
| 275 | -+ | |||
| 100 | +87x |
-
+ moduleServer(id, function(input, output, session) {
|
||
| 276 | -+ | |||
| 101 | +87x |
-
+ logger::log_debug("srv_snapshot_manager_panel initializing")
|
||
| 277 | -86x | +102 | +87x |
- if (length(out)) {
+ setBookmarkExclude(c("show_snapshot_manager"))
|
| 278 | -3x | +103 | +87x |
- paste(out, collapse = "\n")+ observeEvent(input$show_snapshot_manager, {
|
| 279 | -+ | |||
| 104 | +! |
- } else {
+ logger::log_debug("srv_snapshot_manager_panel@1 show_snapshot_manager button has been clicked.")
|
||
| 280 | -83x | +|||
| 105 | +! |
- TRUE+ showModal( |
||
| 281 | -+ | |||
| 106 | +! |
- }+ modalDialog( |
||
| 282 | -+ | |||
| 107 | +! |
- }+ ui_snapshot_manager(session$ns("module")),
|
||
| 283 | -+ | |||
| 108 | +! |
-
+ class = "snapshot_manager_modal", |
||
| 284 | -+ | |||
| 109 | +! |
- #' Function for validating the title parameter of `teal::init`+ size = "m", |
||
| 285 | -+ | |||
| 110 | +! |
- #'+ footer = NULL, |
||
| 286 | -+ | |||
| 111 | +! |
- #' Checks if the input of the title from `teal::init` will create a valid title and favicon tag.+ easyClose = TRUE |
||
| 287 | +112 |
- #' @param shiny_tag (`shiny.tag`) Object to validate for a valid title.+ ) |
||
| 288 | +113 |
- #' @keywords internal+ ) |
||
| 289 | +114 |
- validate_app_title_tag <- function(shiny_tag) {
+ }) |
||
| 290 | -7x | +115 | +87x |
- checkmate::assert_class(shiny_tag, "shiny.tag")+ srv_snapshot_manager("module", slices_global = slices_global)
|
| 291 | -7x | +|||
| 116 | +
- checkmate::assert_true(shiny_tag$name == "head")+ }) |
|||
| 292 | -6x | +|||
| 117 | +
- child_names <- vapply(shiny_tag$children, `[[`, character(1L), "name")+ } |
|||
| 293 | -6x | +|||
| 118 | +
- checkmate::assert_subset(c("title", "link"), child_names, .var.name = "child tags")
+
|
|||
| 294 | -4x | +|||
| 119 | +
- rel_attr <- shiny_tag$children[[which(child_names == "link")]]$attribs$rel+ #' @rdname module_snapshot_manager |
|||
| 295 | -4x | +|||
| 120 | +
- checkmate::assert_subset(+ ui_snapshot_manager <- function(id) {
|
|||
| 296 | -4x | +|||
| 121 | +! |
- rel_attr,+ ns <- NS(id) |
||
| 297 | -4x | +|||
| 122 | +! |
- c("icon", "shortcut icon"),
+ tags$div( |
||
| 298 | -4x | +|||
| 123 | +! |
- .var.name = "Link tag's rel attribute",+ class = "manager_content", |
||
| 299 | -4x | +|||
| 124 | +! |
- empty.ok = FALSE+ tags$div( |
||
| 300 | -+ | |||
| 125 | +! |
- )+ class = "manager_table_row", |
||
| 301 | -+ | |||
| 126 | +! |
- }+ tags$span(tags$b("Snapshot manager")),
|
||
| 302 | -+ | |||
| 127 | +! |
-
+ actionLink(ns("snapshot_add"), label = NULL, icon = icon("fas fa-camera"), title = "add snapshot"),
|
||
| 303 | -+ | |||
| 128 | +! |
- #' Build app title with favicon+ actionLink(ns("snapshot_load"), label = NULL, icon = icon("fas fa-upload"), title = "upload snapshot"),
|
||
| 304 | -+ | |||
| 129 | +! |
- #'+ actionLink(ns("snapshot_reset"), label = NULL, icon = icon("fas fa-undo"), title = "reset initial state"),
|
||
| 305 | -+ | |||
| 130 | +! |
- #' A helper function to create the browser title along with a logo.+ NULL |
||
| 306 | +131 |
- #'+ ), |
||
| 307 | -+ | |||
| 132 | +! |
- #' @param title (`character`) The browser title for the `teal` app.+ uiOutput(ns("snapshot_list"))
|
||
| 308 | +133 |
- #' @param favicon (`character`) The path for the icon for the title.+ ) |
||
| 309 | +134 |
- #' The image/icon path can be remote or the static path accessible by `shiny`, like the `www/`+ } |
||
| 310 | +135 |
- #'+ |
||
| 311 | +136 |
- #' @return A `shiny.tag` containing the element that adds the title and logo to the `shiny` app.+ #' @rdname module_snapshot_manager |
||
| 312 | +137 |
- #' @export+ srv_snapshot_manager <- function(id, slices_global) {
|
||
| 313 | -+ | |||
| 138 | +87x |
- build_app_title <- function(+ checkmate::assert_character(id) |
||
| 314 | +139 |
- title = "teal app",+ |
||
| 315 | -+ | |||
| 140 | +87x |
- favicon = "https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/PNG/nest.png") {
+ moduleServer(id, function(input, output, session) {
|
||
| 316 | -15x | +141 | +87x |
- checkmate::assert_string(title, null.ok = TRUE)+ logger::log_debug("srv_snapshot_manager initializing")
|
| 317 | -15x | +|||
| 142 | +
- checkmate::assert_string(favicon, null.ok = TRUE)+ |
|||
| 318 | -15x | +|||
| 143 | +
- tags$head(+ # Set up bookmarking callbacks ---- |
|||
| 319 | -15x | +|||
| 144 | +
- tags$title(title),+ # Register bookmark exclusions (all buttons and text fields). |
|||
| 320 | -15x | +145 | +87x |
- tags$link(+ setBookmarkExclude(c( |
| 321 | -15x | +146 | +87x |
- rel = "icon",+ "snapshot_add", "snapshot_load", "snapshot_reset", |
| 322 | -15x | +147 | +87x |
- href = favicon,+ "snapshot_name_accept", "snaphot_file_accept", |
| 323 | -15x | +148 | +87x |
- sizes = "any"+ "snapshot_name", "snapshot_file" |
| 324 | +149 |
- )+ )) |
||
| 325 | +150 |
- )+ # Add snapshot history to bookmark. |
||
| 326 | -+ | |||
| 151 | +87x |
- }+ session$onBookmark(function(state) {
|
||
| 327 | -+ | |||
| 152 | +! |
-
+ logger::log_debug("srv_snapshot_manager@onBookmark: storing snapshot and bookmark history")
|
||
| 328 | -+ | |||
| 153 | +! |
- #' Application ID+ state$values$snapshot_history <- snapshot_history() # isolate this? |
||
| 329 | +154 |
- #'+ }) |
||
| 330 | +155 |
- #' Creates App ID used to match filter snapshots to application.+ |
||
| 331 | -+ | |||
| 156 | +87x |
- #'+ ns <- session$ns |
||
| 332 | +157 |
- #' Calculate app ID that will be used to stamp filter state snapshots.+ |
||
| 333 | +158 |
- #' App ID is a hash of the app's data and modules.+ # Track global filter states ---- |
||
| 334 | -+ | |||
| 159 | +87x |
- #' See "transferring snapshots" section in ?snapshot.+ snapshot_history <- reactiveVal({
|
||
| 335 | +160 |
- #'+ # Restore directly from bookmarked state, if applicable. |
||
| 336 | -+ | |||
| 161 | +87x |
- #' @param data (`teal_data` or `teal_data_module`) as accepted by `init`+ restoreValue( |
||
| 337 | -+ | |||
| 162 | +87x |
- #' @param modules (`teal_modules`) object as accepted by `init`+ ns("snapshot_history"),
|
||
| 338 | -+ | |||
| 163 | +87x |
- #'+ list("Initial application state" = shiny::isolate(as.list(slices_global$all_slices(), recursive = TRUE)))
|
||
| 339 | +164 |
- #' @return A single character string.+ ) |
||
| 340 | +165 |
- #'+ }) |
||
| 341 | +166 |
- #' @keywords internal+ |
||
| 342 | +167 |
- create_app_id <- function(data, modules) {
- |
- ||
| 343 | -23x | -
- checkmate::assert_multi_class(data, c("teal_data", "teal_data_module"))
- |
- ||
| 344 | -22x | -
- checkmate::assert_class(modules, "teal_modules")+ # Snapshot current application state ---- |
||
| 345 | +168 |
-
+ # Name snaphsot. |
||
| 346 | -21x | +169 | +87x |
- data <- if (inherits(data, "teal_data")) {
+ observeEvent(input$snapshot_add, {
|
| 347 | -19x | +|||
| 170 | +! |
- as.list(data)+ logger::log_debug("srv_snapshot_manager: snapshot_add button clicked")
|
||
| 348 | -21x | +|||
| 171 | +! |
- } else if (inherits(data, "teal_data_module")) {
+ showModal( |
||
| 349 | -2x | +|||
| 172 | +! |
- deparse1(body(data$server))+ modalDialog( |
||
| 350 | -+ | |||
| 173 | +! |
- }+ textInput(ns("snapshot_name"), "Name the snapshot", width = "100%", placeholder = "Meaningful, unique name"),
|
||
| 351 | -21x | +|||
| 174 | +! |
- modules <- lapply(modules, defunction)+ footer = tagList( |
||
| 352 | -+ | |||
| 175 | +! |
-
+ actionButton(ns("snapshot_name_accept"), "Accept", icon = icon("far fa-thumbs-up")),
|
||
| 353 | -21x | +|||
| 176 | +! |
- rlang::hash(list(data = data, modules = modules))+ modalButton(label = "Cancel", icon = icon("far fa-thumbs-down"))
|
||
| 354 | +177 |
- }+ ), |
||
| 355 | -+ | |||
| 178 | +! |
-
+ size = "s" |
||
| 356 | +179 |
- #' Go through list and extract bodies of encountered functions as string, recursively.+ ) |
||
| 357 | +180 |
- #' @keywords internal+ ) |
||
| 358 | +181 |
- #' @noRd+ }) |
||
| 359 | +182 |
- defunction <- function(x) {
+ # Store snaphsot. |
||
| 360 | -297x | +183 | +87x |
- if (is.list(x)) {
+ observeEvent(input$snapshot_name_accept, {
|
| 361 | -121x | +|||
| 184 | +! |
- lapply(x, defunction)+ logger::log_debug("srv_snapshot_manager: snapshot_name_accept button clicked")
|
||
| 362 | -176x | +|||
| 185 | +! |
- } else if (is.function(x)) {
+ snapshot_name <- trimws(input$snapshot_name) |
||
| 363 | -54x | +|||
| 186 | +! |
- deparse1(body(x))+ if (identical(snapshot_name, "")) {
|
||
| 364 | -+ | |||
| 187 | +! |
- } else {
+ logger::log_debug("srv_snapshot_manager: snapshot name rejected")
|
||
| 365 | -122x | +|||
| 188 | +! |
- x+ showNotification( |
||
| 366 | -+ | |||
| 189 | +! |
- }+ "Please name the snapshot.", |
||
| 367 | -+ | |||
| 190 | +! |
- }+ type = "message" |
||
| 368 | +191 |
-
+ ) |
||
| 369 | -+ | |||
| 192 | +! |
- #' Get unique labels+ updateTextInput(inputId = "snapshot_name", value = "", placeholder = "Meaningful, unique name") |
||
| 370 | -+ | |||
| 193 | +! |
- #'+ } else if (is.element(make.names(snapshot_name), make.names(names(snapshot_history())))) {
|
||
| 371 | -+ | |||
| 194 | +! |
- #' Get unique labels for the modules to avoid namespace conflicts.+ logger::log_debug("srv_snapshot_manager: snapshot name rejected")
|
||
| 372 | -+ | |||
| 195 | +! |
- #'+ showNotification( |
||
| 373 | -+ | |||
| 196 | +! |
- #' @param labels (`character`) vector of labels+ "This name is in conflict with other snapshot names. Please choose a different one.", |
||
| 374 | -+ | |||
| 197 | +! |
- #'+ type = "message" |
||
| 375 | +198 |
- #' @return (`character`) vector of unique labels+ ) |
||
| 376 | -+ | |||
| 199 | +! |
- #'+ updateTextInput(inputId = "snapshot_name", value = "", placeholder = "Meaningful, unique name") |
||
| 377 | +200 |
- #' @keywords internal+ } else {
|
||
| 378 | -+ | |||
| 201 | +! |
- get_unique_labels <- function(labels) {
+ logger::log_debug("srv_snapshot_manager: snapshot name accepted, adding snapshot")
|
||
| 379 | -141x | -
- make.unique(gsub("[^[:alnum:]]", "_", tolower(labels)), sep = "_")
- |
- ||
| 380 | -- |
- }- |
- ||
| 381 | -- | - - | -||
| 382 | -- |
- #' Remove ANSI escape sequences from a string- |
- ||
| 383 | -- |
- #' @noRd- |
- ||
| 384 | -+ | |||
| 202 | +! |
- strip_style <- function(string) {
+ snapshot <- as.list(slices_global$all_slices(), recursive = TRUE) |
||
| 385 | -2x | +|||
| 203 | +! |
- checkmate::assert_string(string)+ snapshot_update <- c(snapshot_history(), list(snapshot)) |
||
| 386 | -+ | |||
| 204 | +! |
-
+ names(snapshot_update)[length(snapshot_update)] <- snapshot_name |
||
| 387 | -2x | +|||
| 205 | +! |
- gsub(+ snapshot_history(snapshot_update) |
||
| 388 | -2x | +|||
| 206 | +! |
- "(?:(?:\\x{001b}\\[)|\\x{009b})(?:(?:[0-9]{1,3})?(?:(?:;[0-9]{0,3})*)?[A-M|f-m])|\\x{001b}[A-M]",
+ removeModal() |
||
| 389 | +207 |
- "",- |
- ||
| 390 | -2x | -
- string,- |
- ||
| 391 | -2x | -
- perl = TRUE,+ # Reopen filter manager modal by clicking button in the main application. |
||
| 392 | -2x | +|||
| 208 | +! |
- useBytes = TRUE+ shinyjs::click(id = "teal-wunder_bar-show_snapshot_manager", asis = TRUE) |
||
| 393 | +209 |
- )+ } |
||
| 394 | +210 |
- }+ }) |
||
| 395 | +211 | |||
| 396 | +212 |
- #' @keywords internal+ # Upload a snapshot file ---- |
||
| 397 | +213 |
- #' @noRd+ # Select file. |
||
| 398 | -4x | -
- pasten <- function(...) paste0(..., "\n")- |
- ||
| 399 | -- | - - | -||
| 400 | -- |
- #' Convert character list to human readable html with commas and "and"- |
- ||
| 401 | -- |
- #' @noRd- |
- ||
| 402 | -- |
- paste_datanames_character <- function(x,- |
- ||
| 403 | -+ | 214 | +87x |
- tags = list(span = shiny::tags$span, code = shiny::tags$code),+ observeEvent(input$snapshot_load, {
|
| 404 | -+ | |||
| 215 | +! |
- tagList = shiny::tagList) { # nolint: object_name.
+ logger::log_debug("srv_snapshot_manager: snapshot_load button clicked")
|
||
| 405 | +216 | ! |
- checkmate::assert_character(x)+ showModal( |
|
| 406 | +217 | ! |
- do.call(+ modalDialog( |
|
| 407 | +218 | ! |
- tagList,+ fileInput(ns("snapshot_file"), "Choose snapshot file", accept = ".json", width = "100%"),
|
|
| 408 | +219 | ! |
- lapply(seq_along(x), function(.ix) {
+ textInput( |
|
| 409 | +220 | ! |
- tagList(+ ns("snapshot_name"),
|
|
| 410 | +221 | ! |
- tags$code(x[.ix]),+ "Name the snapshot (optional)", |
|
| 411 | +222 | ! |
- if (.ix != length(x)) {
+ width = "100%", |
|
| 412 | +223 | ! |
- tags$span(if (.ix == length(x) - 1) " and " else ", ")+ placeholder = "Meaningful, unique name" |
|
| 413 | +224 |
- }+ ), |
||
| 414 | -+ | |||
| 225 | +! |
- )+ footer = tagList( |
||
| 415 | -+ | |||
| 226 | +! |
- })+ actionButton(ns("snaphot_file_accept"), "Accept", icon = icon("far fa-thumbs-up")),
|
||
| 416 | -+ | |||
| 227 | +! |
- )+ modalButton(label = "Cancel", icon = icon("far fa-thumbs-down"))
|
||
| 417 | +228 |
- }+ ) |
||
| 418 | +229 |
-
+ ) |
||
| 419 | +230 |
- #' Build datanames error string for error message+ ) |
||
| 420 | +231 |
- #'+ }) |
||
| 421 | +232 |
- #' tags and tagList are overwritten in arguments allowing to create strings for+ # Store new snapshot to list and restore filter states. |
||
| 422 | -+ | |||
| 233 | +87x |
- #' logging purposes+ observeEvent(input$snaphot_file_accept, {
|
||
| 423 | -+ | |||
| 234 | +! |
- #' @noRd+ logger::log_debug("srv_snapshot_manager: snapshot_file_accept button clicked")
|
||
| 424 | -+ | |||
| 235 | +! |
- build_datanames_error_message <- function(label = NULL,+ snapshot_name <- trimws(input$snapshot_name) |
||
| 425 | -+ | |||
| 236 | +! |
- datanames,+ if (identical(snapshot_name, "")) {
|
||
| 426 | -+ | |||
| 237 | +! |
- extra_datanames,+ logger::log_debug("srv_snapshot_manager: no snapshot name provided, naming after file")
|
||
| 427 | -+ | |||
| 238 | +! |
- tags = list(span = shiny::tags$span, code = shiny::tags$code),+ snapshot_name <- tools::file_path_sans_ext(input$snapshot_file$name) |
||
| 428 | +239 |
- tagList = shiny::tagList) { # nolint: object_name.
+ } |
||
| 429 | +240 | ! |
- tags$span(+ if (is.element(make.names(snapshot_name), make.names(names(snapshot_history())))) {
|
|
| 430 | +241 | ! |
- tags$span(pluralize(extra_datanames, "Dataset")),+ logger::log_debug("srv_snapshot_manager: snapshot name rejected")
|
|
| 431 | +242 | ! |
- paste_datanames_character(extra_datanames, tags, tagList),+ showNotification( |
|
| 432 | +243 | ! |
- tags$span(+ "This name is in conflict with other snapshot names. Please choose a different one.", |
|
| 433 | +244 | ! |
- sprintf(+ type = "message" |
|
| 434 | -! | +|||
| 245 | +
- "%s missing%s",+ ) |
|||
| 435 | +246 | ! |
- pluralize(extra_datanames, "is", "are"),+ updateTextInput(inputId = "snapshot_name", value = "", placeholder = "Meaningful, unique name") |
|
| 436 | -! | +|||
| 247 | +
- if (is.null(label)) "" else sprintf(" for tab '%s'", label)
+ } else {
|
|||
| 437 | +248 |
- )+ # Restore snapshot and verify app compatibility. |
||
| 438 | -+ | |||
| 249 | +! |
- ),+ logger::log_debug("srv_snapshot_manager: snapshot name accepted, loading snapshot")
|
||
| 439 | +250 | ! |
- if (length(datanames) >= 1) {
+ snapshot_state <- try(slices_restore(input$snapshot_file$datapath)) |
|
| 440 | +251 | ! |
- tagList(+ if (!inherits(snapshot_state, "modules_teal_slices")) {
|
|
| 441 | +252 | ! |
- tags$span(pluralize(datanames, "Dataset")),+ logger::log_debug("srv_snapshot_manager: snapshot file corrupt")
|
|
| 442 | +253 | ! |
- tags$span("available in data:"),
+ showNotification( |
|
| 443 | +254 | ! |
- tagList(+ "File appears to be corrupt.", |
|
| 444 | +255 | ! |
- tags$span(+ type = "error"+ |
+ |
| 256 | ++ |
+ ) |
||
| 445 | +257 | ! |
- paste_datanames_character(datanames, tags, tagList),+ } else if (!identical(attr(snapshot_state, "app_id"), attr(slices_global$all_slices(), "app_id"))) {
|
|
| 446 | +258 | ! |
- tags$span(".", .noWS = "outside"),
+ logger::log_debug("srv_snapshot_manager: snapshot not compatible with app")
|
|
| 447 | +259 | ! |
- .noWS = c("outside")
+ showNotification( |
|
| 448 | -+ | |||
| 260 | +! |
- )+ "This snapshot file is not compatible with the app and cannot be loaded.",+ |
+ ||
| 261 | +! | +
+ type = "warning" |
||
| 449 | +262 |
- )+ ) |
||
| 450 | +263 |
- )+ } else {
|
||
| 451 | +264 |
- } else {
+ # Add to snapshot history. |
||
| 452 | +265 | ! |
- tags$span("No datasets are available in data.")
+ logger::log_debug("srv_snapshot_manager: snapshot loaded, adding to history")
|
|
| 453 | -+ | |||
| 266 | +! |
- }+ snapshot <- as.list(slices_global$all_slices(), recursive = TRUE) |
||
| 454 | -+ | |||
| 267 | +! |
- )+ snapshot_update <- c(snapshot_history(), list(snapshot)) |
||
| 455 | -+ | |||
| 268 | +! |
- }+ names(snapshot_update)[length(snapshot_update)] <- snapshot_name |
||
| 456 | -+ | |||
| 269 | +! |
-
+ snapshot_history(snapshot_update) |
||
| 457 | +270 |
- #' Smart `rbind`+ ### Begin simplified restore procedure. ### |
||
| 458 | -+ | |||
| 271 | +! |
- #'+ logger::log_debug("srv_snapshot_manager: restoring snapshot")
|
||
| 459 | -+ | |||
| 272 | +! |
- #' Combine `data.frame` objects which have different columns+ slices_global$slices_set(snapshot_state) |
||
| 460 | -+ | |||
| 273 | +! |
- #'+ removeModal() |
||
| 461 | +274 |
- #' @param ... (`data.frame`)+ ### End simplified restore procedure. ### |
||
| 462 | +275 |
- #' @keywords internal+ } |
||
| 463 | +276 |
- .smart_rbind <- function(...) {
- |
- ||
| 464 | -89x | -
- dots <- list(...)- |
- ||
| 465 | -89x | -
- checkmate::assert_list(dots, "data.frame", .var.name = "...")- |
- ||
| 466 | -89x | -
- Reduce(- |
- ||
| 467 | -89x | -
- x = dots,- |
- ||
| 468 | -89x | -
- function(x, y) {
- |
- ||
| 469 | -72x | -
- all_columns <- union(colnames(x), colnames(y))- |
- ||
| 470 | -72x | -
- x[setdiff(all_columns, colnames(x))] <- NA- |
- ||
| 471 | -72x | -
- y[setdiff(all_columns, colnames(y))] <- NA- |
- ||
| 472 | -72x | -
- rbind(x, y)- |
- ||
| 473 | -- |
- }- |
- ||
| 474 | -- |
- )- |
- ||
| 475 | -- |
- }- |
- ||
| 476 | -- | - - | -||
| 477 | -- |
- #' Pluralize a word depending on the size of the input- |
- ||
| 478 | -- |
- #'- |
- ||
| 479 | -- |
- #' @param x (`object`) to check length for plural.- |
- ||
| 480 | -- |
- #' @param singular (`character`) singular form of the word.- |
- ||
| 481 | -- |
- #' @param plural (optional `character`) plural form of the word. If not given an "s"- |
- ||
| 482 | -- |
- #' is added to the singular form.- |
- ||
| 483 | -- |
- #'- |
- ||
| 484 | -- |
- #' @return A `character` that correctly represents the size of the `x` argument.- |
- ||
| 485 | -- |
- #' @keywords internal- |
- ||
| 486 | -- |
- pluralize <- function(x, singular, plural = NULL) {
- |
- ||
| 487 | -70x | -
- checkmate::assert_string(singular)- |
- ||
| 488 | -70x | -
- checkmate::assert_string(plural, null.ok = TRUE)- |
- ||
| 489 | -70x | -
- if (length(x) == 1L) { # Zero length object should use plural form.
- |
- ||
| 490 | -42x | -
- singular- |
- ||
| 491 | -- |
- } else {
- |
- ||
| 492 | -28x | -
- if (is.null(plural)) {
- |
- ||
| 493 | -12x | -
- sprintf("%ss", singular)
- |
- ||
| 494 | -- |
- } else {
- |
- ||
| 495 | -16x | -
- plural- |
- ||
| 496 | -- |
- }- |
- ||
| 497 | -- |
- }- |
- ||
| 498 | -- |
- }- |
-
| 1 | -- |
- #' Create a `teal` module for previewing a report- |
-
| 2 | -- |
- #'- |
-
| 3 | -- |
- #' @description `r lifecycle::badge("experimental")`
- |
-
| 4 | -- |
- #'- |
-
| 5 | -- |
- #' This function wraps [teal.reporter::reporter_previewer_ui()] and- |
-
| 6 | -- |
- #' [teal.reporter::reporter_previewer_srv()] into a `teal_module` to be- |
-
| 7 | -- |
- #' used in `teal` applications.- |
-
| 8 | -- |
- #'- |
-
| 9 | -- |
- #' If you are creating a `teal` application using [init()] then this- |
-
| 10 | -- |
- #' module will be added to your application automatically if any of your `teal_modules`- |
-
| 11 | -- |
- #' support report generation.- |
-
| 12 | -- |
- #'- |
-
| 13 | -- |
- #' @inheritParams teal_modules- |
-
| 14 | -- |
- #' @param server_args (named `list`)- |
-
| 15 | -- |
- #' Arguments passed to [teal.reporter::reporter_previewer_srv()].- |
-
| 16 | -- |
- #'- |
-
| 17 | -- |
- #' @return- |
-
| 18 | -- |
- #' `teal_module` (extended with `teal_module_previewer` class) containing the `teal.reporter` previewer functionality.- |
-
| 19 | -- |
- #'- |
-
| 20 | -- |
- #' @export- |
-
| 21 | -- |
- #'- |
-
| 22 | -- |
- reporter_previewer_module <- function(label = "Report previewer", server_args = list()) {
- |
-
| 23 | -7x | -
- checkmate::assert_string(label)- |
-
| 24 | -5x | -
- checkmate::assert_list(server_args, names = "named")- |
-
| 25 | -5x | -
- checkmate::assert_true(all(names(server_args) %in% names(formals(teal.reporter::reporter_previewer_srv))))- |
-
| 26 | -- | - - | -
| 27 | -3x | -
- message("Initializing reporter_previewer_module")
- |
-
| 28 | -- | - - | -
| 29 | -3x | -
- srv <- function(id, reporter, ...) {
- |
-
| 30 | -! | -
- teal.reporter::reporter_previewer_srv(id, reporter, ...)- |
-
| 31 | -- |
- }- |
-
| 32 | -- | - - | -
| 33 | -3x | -
- ui <- function(id, ...) {
- |
-
| 34 | -! | -
- teal.reporter::reporter_previewer_ui(id, ...)- |
-
| 35 | -- |
- }- |
-
| 36 | -- | - - | -
| 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 | -- |
- )- |
-
| 42 | -- |
- # Module is created with a placeholder label and the label is changed later.- |
-
| 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 | -- |
- }- |
-
| 1 | -- |
- #' Data Module for teal- |
- ||
| 2 | -- |
- #'- |
- ||
| 3 | -- |
- #' This module manages the `data` argument for `srv_teal`. The `teal` framework uses [teal.data::teal_data()],- |
- ||
| 4 | -- |
- #' which can be provided in various ways:- |
- ||
| 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.- |
- ||
| 7 | -- |
- #'- |
- ||
| 8 | -- |
- #' @details- |
- ||
| 9 | -- |
- #' ## Reactive `teal_data`:- |
- ||
| 10 | -- |
- #'- |
- ||
| 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`:- |
- ||
| 13 | -- |
- #' 1. Using a `reactive` object provided from outside the `teal` application. In this scenario,- |
- ||
| 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- |
- ||
| 16 | -- |
- #' be resubmitted by the user as needed.- |
- ||
| 17 | -- |
- #'- |
- ||
| 18 | -- |
- #' Since the server of [teal_data_module()] must return a `reactive` `teal_data` object, both- |
- ||
| 19 | -- |
- #' 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 | -- |
- #' involves control from a custom module within the app.- |
- ||
| 22 | -- |
- #'- |
- ||
| 23 | -- |
- #' For more details, see [`module_teal_data`].- |
- ||
| 24 | -- |
- #'- |
- ||
| 25 | -- |
- #' @inheritParams init- |
- ||
| 26 | -- |
- #'- |
- ||
| 27 | -- |
- #' @param data (`teal_data`, `teal_data_module`, or `reactive` returning `teal_data`)- |
- ||
| 28 | -- |
- #' The data which application will depend on.- |
- ||
| 29 | -- |
- #'- |
- ||
| 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.- |
- ||
| 33 | -- |
- #'- |
- ||
| 34 | -- |
- #' @rdname module_init_data- |
- ||
| 35 | -- |
- #' @name module_init_data- |
- ||
| 36 | -- |
- #' @keywords internal- |
- ||
| 37 | -- |
- NULL- |
- ||
| 38 | -- | - - | -||
| 39 | -- |
- #' @rdname module_init_data- |
- ||
| 40 | -- |
- ui_init_data <- function(id) {
- |
- ||
| 41 | -9x | -
- ns <- shiny::NS(id)- |
- ||
| 42 | -9x | -
- shiny::div(- |
- ||
| 43 | -9x | -
- id = ns("content"),
- |
- ||
| 44 | -9x | -
- style = "display: inline-block; width: 100%;",- |
- ||
| 45 | -9x | -
- uiOutput(ns("data"))
- |
- ||
| 46 | -- |
- )- |
- ||
| 47 | -- |
- }- |
- ||
| 48 | -- | - - | -||
| 49 | -- |
- #' @rdname module_init_data- |
- ||
| 50 | -- |
- srv_init_data <- function(id, data) {
- |
- ||
| 51 | -88x | -
- checkmate::assert_character(id, max.len = 1, any.missing = FALSE)- |
- ||
| 52 | -88x | -
- checkmate::assert_multi_class(data, c("teal_data", "teal_data_module", "reactive"))
- |
- ||
| 53 | -- | - - | -||
| 54 | -88x | -
- moduleServer(id, function(input, output, session) {
- |
- ||
| 55 | -88x | -
- logger::log_debug("srv_data initializing.")
- |
- ||
| 56 | -- |
- # data_rv contains teal_data object- |
- ||
| 57 | -- |
- # either passed to teal::init or returned from teal_data_module- |
- ||
| 58 | -88x | -
- data_out <- if (inherits(data, "teal_data_module")) {
- |
- ||
| 59 | -10x | -
- output$data <- renderUI(data$ui(id = session$ns("teal_data_module")))
- |
- ||
| 60 | -10x | -
- data$server("teal_data_module")
- |
- ||
| 61 | -88x | -
- } else if (inherits(data, "teal_data")) {
- |
- ||
| 62 | -48x | -
- reactiveVal(data)- |
- ||
| 63 | -88x | -
- } else if (test_reactive(data)) {
- |
- ||
| 64 | -30x | -
- data- |
- ||
| 65 | -- |
- }- |
- ||
| 66 | -- | - - | -||
| 67 | -87x | -
- data_handled <- reactive({
- |
- ||
| 68 | -80x | -
- tryCatch(data_out(), error = function(e) e)+ } |
||
| 69 | +277 |
}) |
||
| 70 | +278 |
-
+ # Apply newly added snapshot. |
||
| 71 | +279 |
- # We want to exclude teal_data_module elements from bookmarking as they might have some secrets+ |
||
| 72 | -87x | +|||
| 280 | +
- observeEvent(data_handled(), {
+ # Restore initial state ---- |
|||
| 73 | -80x | +281 | +87x |
- if (inherits(data_handled(), "teal_data")) {
+ observeEvent(input$snapshot_reset, {
|
| 74 | -75x | +282 | +2x |
- app_session <- .subset2(shiny::getDefaultReactiveDomain(), "parent")+ logger::log_debug("srv_snapshot_manager: snapshot_reset button clicked, restoring snapshot")
|
| 75 | -75x | +283 | +2x |
- setBookmarkExclude(+ s <- "Initial application state" |
| 76 | -75x | +|||
| 284 | +
- session$ns(+ ### Begin restore procedure. ### |
|||
| 77 | -75x | +285 | +2x |
- grep(+ snapshot <- snapshot_history()[[s]] |
| 78 | -75x | +286 | +2x |
- pattern = "teal_data_module-",+ snapshot_state <- as.teal_slices(snapshot) |
| 79 | -75x | +287 | +2x |
- x = names(reactiveValuesToList(input)),+ slices_global$slices_set(snapshot_state) |
| 80 | -75x | +288 | +2x |
- value = TRUE+ removeModal() |
| 81 | +289 |
- )+ ### End restore procedure. ### |
||
| 82 | +290 |
- ),+ }) |
||
| 83 | -75x | +|||
| 291 | +
- session = app_session+ |
|||
| 84 | +292 |
- )+ # Build snapshot table ---- |
||
| 85 | +293 |
- }+ # Create UI elements and server logic for the snapshot table. |
||
| 86 | +294 |
- })+ # Observers must be tracked to avoid duplication and excess reactivity. |
||
| 87 | +295 |
-
+ # Remaining elements are tracked likewise for consistency and a slight speed margin. |
||
| 88 | +296 | 87x |
- data_handled+ observers <- reactiveValues() |
|
| 89 | -+ | |||
| 297 | +87x |
- })+ handlers <- reactiveValues() |
||
| 90 | -+ | |||
| 298 | +87x |
- }+ divs <- reactiveValues() |
||
| 91 | +299 | |||
| 92 | -+ | |||
| 300 | +87x |
- #' Adds signature protection to the `datanames` in the data+ observeEvent(snapshot_history(), {
|
||
| 93 | -+ | |||
| 301 | +77x |
- #' @param data (`teal_data`)+ logger::log_debug("srv_snapshot_manager: snapshot history modified, updating snapshot list")
|
||
| 94 | -+ | |||
| 302 | +77x |
- #' @return `teal_data` with additional code that has signature of the `datanames`+ lapply(names(snapshot_history())[-1L], function(s) {
|
||
| 95 | -+ | |||
| 303 | +! |
- #' @keywords internal+ id_pickme <- sprintf("pickme_%s", make.names(s))
|
||
| 96 | -+ | |||
| 304 | +! |
- .add_signature_to_data <- function(data) {
+ id_saveme <- sprintf("saveme_%s", make.names(s))
|
||
| 97 | -75x | +|||
| 305 | +! |
- hashes <- .get_hashes_code(data)+ id_rowme <- sprintf("rowme_%s", make.names(s))
|
||
| 98 | -75x | +|||
| 306 | +
- tdata <- do.call(+ |
|||
| 99 | -75x | +|||
| 307 | +
- teal.data::teal_data,+ # Observer for restoring snapshot. |
|||
| 100 | -75x | +|||
| 308 | +! |
- c(+ if (!is.element(id_pickme, names(observers))) {
|
||
| 101 | -75x | +|||
| 309 | +! |
- list(code = trimws(c(teal.code::get_code(data), hashes), which = "right")),+ observers[[id_pickme]] <- observeEvent(input[[id_pickme]], {
|
||
| 102 | -75x | +|||
| 310 | +
- list(join_keys = teal.data::join_keys(data)),+ ### Begin restore procedure. ### |
|||
| 103 | -75x | +|||
| 311 | +! |
- sapply(+ snapshot <- snapshot_history()[[s]] |
||
| 104 | -75x | +|||
| 312 | +! |
- names(data),+ snapshot_state <- as.teal_slices(snapshot) |
||
| 105 | -75x | +|||
| 313 | +
- teal.code::get_var,+ |
|||
| 106 | -75x | +|||
| 314 | +! |
- object = data,+ slices_global$slices_set(snapshot_state) |
||
| 107 | -75x | +|||
| 315 | +! |
- simplify = FALSE+ removeModal() |
||
| 108 | +316 |
- )+ ### End restore procedure. ### |
||
| 109 | +317 |
- )+ }) |
||
| 110 | +318 |
- )+ } |
||
| 111 | +319 |
-
+ # Create handler for downloading snapshot. |
||
| 112 | -75x | +|||
| 320 | +! |
- tdata@verified <- data@verified+ if (!is.element(id_saveme, names(handlers))) {
|
||
| 113 | -75x | +|||
| 321 | +! |
- tdata+ output[[id_saveme]] <- downloadHandler( |
||
| 114 | -+ | |||
| 322 | +! |
- }+ filename = function() {
|
||
| 115 | -+ | |||
| 323 | +! |
-
+ sprintf("teal_snapshot_%s_%s.json", s, Sys.Date())
|
||
| 116 | +324 |
- #' Get code that tests the integrity of the reproducible data+ }, |
||
| 117 | -+ | |||
| 325 | +! |
- #'+ content = function(file) {
|
||
| 118 | -+ | |||
| 326 | +! |
- #' @param data (`teal_data`) object holding the data+ snapshot <- snapshot_history()[[s]] |
||
| 119 | -+ | |||
| 327 | +! |
- #' @param datanames (`character`) names of `datasets`+ snapshot_state <- as.teal_slices(snapshot) |
||
| 120 | -+ | |||
| 328 | +! |
- #'+ slices_store(tss = snapshot_state, file = file) |
||
| 121 | +329 |
- #' @return A character vector with the code lines.+ } |
||
| 122 | +330 |
- #' @keywords internal+ )+ |
+ ||
| 331 | +! | +
+ handlers[[id_saveme]] <- id_saveme |
||
| 123 | +332 |
- #'+ } |
||
| 124 | +333 |
- .get_hashes_code <- function(data, datanames = names(data)) {
+ # Create a row for the snapshot table. |
||
| 125 | -75x | +|||
| 334 | +! |
- vapply(+ if (!is.element(id_rowme, names(divs))) {
|
||
| 126 | -75x | +|||
| 335 | +! |
- datanames,+ divs[[id_rowme]] <- tags$div( |
||
| 127 | -75x | +|||
| 336 | +! |
- function(dataname, datasets) {
+ class = "manager_table_row", |
||
| 128 | -133x | +|||
| 337 | +! |
- x <- data[[dataname]]+ tags$span(tags$h5(s)), |
||
| 129 | -+ | |||
| 338 | +! |
-
+ actionLink(inputId = ns(id_pickme), label = icon("far fa-circle-check"), title = "select"),
|
||
| 130 | -133x | +|||
| 339 | +! |
- code <- if (is.function(x) && !is.primitive(x)) {
+ downloadLink(outputId = ns(id_saveme), label = icon("far fa-save"), title = "save to file")
|
||
| 131 | -6x | +|||
| 340 | +
- x <- deparse1(x)+ ) |
|||
| 132 | -6x | +|||
| 341 | +
- bquote(rlang::hash(deparse1(.(as.name(dataname)))))+ } |
|||
| 133 | +342 |
- } else {
+ }) |
||
| 134 | -127x | +|||
| 343 | +
- bquote(rlang::hash(.(as.name(dataname))))+ }) |
|||
| 135 | +344 |
- }+ + |
+ ||
| 345 | ++ |
+ # Create table to display list of snapshots and their actions. |
||
| 136 | -133x | +346 | +87x |
- sprintf(+ output$snapshot_list <- renderUI({
|
| 137 | -133x | +347 | +77x |
- "stopifnot(%s == %s) # @linksto %s",+ rows <- rev(reactiveValuesToList(divs)) |
| 138 | -133x | +348 | +77x |
- deparse1(code),+ if (length(rows) == 0L) {
|
| 139 | -133x | +349 | +77x |
- deparse1(rlang::hash(x)),+ tags$div( |
| 140 | -133x | +350 | +77x |
- dataname+ class = "manager_placeholder",+ |
+
| 351 | +77x | +
+ "Snapshots will appear here." |
||
| 141 | +352 |
- )+ ) |
||
| 142 | +353 |
- },+ } else {
|
||
| 143 | -75x | +|||
| 354 | +! | +
+ rows+ |
+ ||
| 355 | ++ |
+ }+ |
+ ||
| 356 | ++ |
+ })+ |
+ ||
| 357 | +
- character(1L),+ |
|||
| 144 | -75x | +358 | +87x |
- USE.NAMES = TRUE+ snapshot_history |
| 145 | +359 |
- )+ }) |
||
| 146 | +360 |
}@@ -8395,973 +7424,973 @@ teal coverage - 60.11% |
| 1 |
- #' Filter state snapshot management+ #' @title `TealReportCard` |
||
| 2 |
- #'+ #' @description `r lifecycle::badge("experimental")`
|
||
| 3 |
- #' Capture and restore snapshots of the global (app) filter state.+ #' Child class of [`teal.reporter::ReportCard`] that is used for `teal` specific applications. |
||
| 4 |
- #'+ #' In addition to the parent methods, it supports rendering `teal` specific elements such as |
||
| 5 |
- #' This module introduces snapshots: stored descriptions of the filter state of the entire application.+ #' the source code, the encodings panel content and the filter panel content as part of the |
||
| 6 |
- #' Snapshots allow the user to save the current filter state of the application for later use in the session,+ #' meta data. |
||
| 7 |
- #' as well as to save it to file in order to share it with an app developer or other users,+ #' @export |
||
| 8 |
- #' who in turn can upload it to their own session.+ #' |
||
| 9 |
- #'+ TealReportCard <- R6::R6Class( # nolint: object_name. |
||
| 10 |
- #' The snapshot manager is accessed with the camera icon in the tabset bar.+ classname = "TealReportCard", |
||
| 11 |
- #' At the beginning of a session it presents three icons: a camera, an upload, and an circular arrow.+ inherit = teal.reporter::ReportCard, |
||
| 12 |
- #' Clicking the camera captures a snapshot, clicking the upload adds a snapshot from a file+ public = list( |
||
| 13 |
- #' and applies the filter states therein, and clicking the arrow resets initial application state.+ #' @description Appends the source code to the `content` meta data of this `TealReportCard`. |
||
| 14 |
- #' As snapshots are added, they will show up as rows in a table and each will have a select button and a save button.+ #' |
||
| 15 |
- #'+ #' @param src (`character(1)`) code as text. |
||
| 16 |
- #' @section Server logic:+ #' @param ... any `rmarkdown` `R` chunk parameter and its value. |
||
| 17 |
- #' Snapshots are basically `teal_slices` objects, however, since each module is served by a separate instance+ #' But `eval` parameter is always set to `FALSE`. |
||
| 18 |
- #' of `FilteredData` and these objects require shared state, `teal_slice` is a `reactiveVal` so `teal_slices`+ #' @return Object of class `TealReportCard`, invisibly. |
||
| 19 |
- #' cannot be stored as is. Therefore, `teal_slices` are reversibly converted to a list of lists representation+ #' @examples |
||
| 20 |
- #' (attributes are maintained).+ #' card <- TealReportCard$new()$append_src( |
||
| 21 |
- #'+ #' "plot(iris)" |
||
| 22 |
- #' Snapshots are stored in a `reactiveVal` as a named list.+ #' ) |
||
| 23 |
- #' The first snapshot is the initial state of the application and the user can add a snapshot whenever they see fit.+ #' card$get_content()[[1]]$get_content() |
||
| 24 |
- #'+ append_src = function(src, ...) {
|
||
| 25 | -+ | 4x |
- #' For every snapshot except the initial one, a piece of UI is generated that contains+ checkmate::assert_character(src, min.len = 0, max.len = 1) |
| 26 | -+ | 4x |
- #' the snapshot name, a select button to restore that snapshot, and a save button to save it to a file.+ params <- list(...) |
| 27 | -+ | 4x |
- #' The initial snapshot is restored by a separate "reset" button.+ params$eval <- FALSE |
| 28 | -+ | 4x |
- #' It cannot be saved directly but a user is welcome to capture the initial state as a snapshot and save that.+ rblock <- RcodeBlock$new(src) |
| 29 | -+ | 4x |
- #'+ rblock$set_params(params) |
| 30 | -+ | 4x |
- #' @section Snapshot mechanics:+ self$append_content(rblock) |
| 31 | -+ | 4x |
- #' When a snapshot is captured, the user is prompted to name it.+ self$append_metadata("SRC", src)
|
| 32 | -+ | 4x |
- #' Names are displayed as is but since they are used to create button ids,+ invisible(self) |
| 33 |
- #' under the hood they are converted to syntactically valid strings.+ }, |
||
| 34 |
- #' New snapshot names are validated so that their valid versions are unique.+ #' @description Appends the filter state list to the `content` and `metadata` of this `TealReportCard`. |
||
| 35 |
- #' Leading and trailing white space is trimmed.+ #' If the filter state list has an attribute named `formatted`, it appends it to the card otherwise it uses |
||
| 36 |
- #'+ #' the default `yaml::as.yaml` to format the list. |
||
| 37 |
- #' The module can read the global state of the application from `slices_global` and `mapping_matrix`.+ #' If the filter state list is empty, nothing is appended to the `content`. |
||
| 38 |
- #' The former provides a list of all existing `teal_slice`s and the latter says which slice is active in which module.+ #' |
||
| 39 |
- #' Once a name has been accepted, `slices_global` is converted to a list of lists - a snapshot.+ #' @param fs (`teal_slices`) object returned from [teal_slices()] function. |
||
| 40 |
- #' The snapshot contains the `mapping` attribute of the initial application state+ #' @return `self`, invisibly. |
||
| 41 |
- #' (or one that has been restored), which may not reflect the current one,+ append_fs = function(fs) {
|
||
| 42 | -+ | 5x |
- #' so `mapping_matrix` is transformed to obtain the current mapping, i.e. a list that,+ checkmate::assert_class(fs, "teal_slices") |
| 43 | -+ | 4x |
- #' when passed to the `mapping` argument of [teal_slices()], would result in the current mapping.+ self$append_text("Filter State", "header3")
|
| 44 | -+ | 4x |
- #' This is substituted as the snapshot's `mapping` attribute and the snapshot is added to the snapshot list.+ if (length(fs)) {
|
| 45 | -+ | 3x |
- #'+ self$append_content(TealSlicesBlock$new(fs)) |
| 46 |
- #' To restore app state, a snapshot is retrieved from storage and rebuilt into a `teal_slices` object.+ } else {
|
||
| 47 | -+ | 1x |
- #' Then state of all `FilteredData` objects (provided in `datasets`) is cleared+ self$append_text("No filters specified.")
|
| 48 |
- #' and set anew according to the `mapping` attribute of the snapshot.+ } |
||
| 49 | -+ | 4x |
- #' The snapshot is then set as the current content of `slices_global`.+ invisible(self) |
| 50 |
- #'+ }, |
||
| 51 |
- #' To save a snapshot, the snapshot is retrieved and reassembled just like for restoring,+ #' @description Appends the encodings list to the `content` and `metadata` of this `TealReportCard`. |
||
| 52 |
- #' and then saved to file with [slices_store()].+ #' |
||
| 53 |
- #'+ #' @param encodings (`list`) list of encodings selections of the `teal` app. |
||
| 54 |
- #' When a snapshot is uploaded, it will first be added to storage just like a newly created one,+ #' @return `self`, invisibly. |
||
| 55 |
- #' and then used to restore app state much like a snapshot taken from storage.+ #' @examples |
||
| 56 |
- #' Upon clicking the upload icon the user will be prompted for a file to upload+ #' card <- TealReportCard$new()$append_encodings(list(variable1 = "X")) |
||
| 57 |
- #' and may choose to name the new snapshot. The name defaults to the name of the file (the extension is dropped)+ #' card$get_content()[[1]]$get_content() |
||
| 58 |
- #' and normal naming rules apply. Loading the file yields a `teal_slices` object,+ #' |
||
| 59 |
- #' which is disassembled for storage and used directly for restoring app state.+ append_encodings = function(encodings) {
|
||
| 60 | -+ | 4x |
- #'+ checkmate::assert_list(encodings) |
| 61 | -+ | 4x |
- #' @section Transferring snapshots:+ self$append_text("Selected Options", "header3")
|
| 62 | -+ | 4x |
- #' Snapshots uploaded from disk should only be used in the same application they come from,+ if (requireNamespace("yaml", quietly = TRUE)) {
|
| 63 | -+ | 4x |
- #' _i.e._ an application that uses the same data and the same modules.+ self$append_text(yaml::as.yaml(encodings, handlers = list( |
| 64 | -+ | 4x |
- #' To ensure this is the case, `init` stamps `teal_slices` with an app id that is stored in the `app_id` attribute of+ POSIXct = function(x) format(x, "%Y-%m-%d"), |
| 65 | -+ | 4x |
- #' a `teal_slices` object. When a snapshot is restored from file, its `app_id` is compared to that+ POSIXlt = function(x) format(x, "%Y-%m-%d"), |
| 66 | -+ | 4x |
- #' of the current app state and only if the match is the snapshot admitted to the session.+ Date = function(x) format(x, "%Y-%m-%d") |
| 67 | -+ | 4x |
- #'+ )), "verbatim") |
| 68 |
- #' @section Bookmarks:+ } else {
|
||
| 69 | -+ | ! |
- #' An `onBookmark` callback creates a snapshot of the current filter state.+ stop("yaml package is required to format the encodings list")
|
| 70 |
- #' This is done on the app session, not the module session.+ } |
||
| 71 | -+ | 4x |
- #' (The snapshot will be retrieved by `module_teal` in order to set initial app state in a restored app.)+ self$append_metadata("Encodings", encodings)
|
| 72 | -+ | 4x |
- #' Then that snapshot, and the previous snapshot history are dumped into the `values.rds` file in `<bookmark_dir>`.+ invisible(self) |
| 73 |
- #'+ } |
||
| 74 |
- #' @param id (`character(1)`) `shiny` module instance id.+ ), |
||
| 75 |
- #' @param slices_global (`reactiveVal`) that contains a `teal_slices` object+ private = list( |
||
| 76 |
- #' containing all `teal_slice`s existing in the app, both active and inactive.+ dispatch_block = function(block_class) {
|
||
| 77 | -+ | ! |
- #'+ eval(str2lang(block_class)) |
| 78 |
- #' @return `list` containing the snapshot history, where each element is an unlisted `teal_slices` object.+ } |
||
| 79 |
- #'+ ) |
||
| 80 |
- #' @name module_snapshot_manager+ ) |
||
| 81 |
- #' @rdname module_snapshot_manager+ |
||
| 82 |
- #'+ #' @title `TealSlicesBlock` |
||
| 83 |
- #' @author Aleksander Chlebowski+ #' @docType class |
||
| 84 |
- #' @keywords internal+ #' @description |
||
| 85 |
- NULL+ #' Specialized `TealSlicesBlock` block for managing filter panel content in reports. |
||
| 86 |
-
+ #' @keywords internal |
||
| 87 |
- #' @rdname module_snapshot_manager+ TealSlicesBlock <- R6::R6Class( # nolint: object_name_linter. |
||
| 88 |
- ui_snapshot_manager_panel <- function(id) {
+ classname = "TealSlicesBlock", |
||
| 89 | -! | +
- ns <- NS(id)+ inherit = teal.reporter:::TextBlock, |
|
| 90 | -! | +
- tags$button(+ public = list( |
|
| 91 | -! | +
- id = ns("show_snapshot_manager"),
+ #' @description Returns a `TealSlicesBlock` object. |
|
| 92 | -! | +
- class = "btn action-button wunder_bar_button",+ #' |
|
| 93 | -! | +
- title = "View filter mapping",+ #' @details Returns a `TealSlicesBlock` object with no content and no parameters. |
|
| 94 | -! | +
- suppressMessages(icon("fas fa-camera"))
+ #' |
|
| 95 |
- )+ #' @param content (`teal_slices`) object returned from [teal_slices()] function. |
||
| 96 |
- }+ #' @param style (`character(1)`) string specifying style to apply. |
||
| 97 |
-
+ #' |
||
| 98 |
- #' @rdname module_snapshot_manager+ #' @return Object of class `TealSlicesBlock`, invisibly. |
||
| 99 |
- srv_snapshot_manager_panel <- function(id, slices_global) {
+ #' |
||
| 100 | -87x | +
- moduleServer(id, function(input, output, session) {
+ initialize = function(content = teal_slices(), style = "verbatim") {
|
|
| 101 | -87x | +9x |
- logger::log_debug("srv_snapshot_manager_panel initializing")
+ self$set_content(content) |
| 102 | -87x | +8x |
- setBookmarkExclude(c("show_snapshot_manager"))
+ self$set_style(style) |
| 103 | -87x | +8x |
- observeEvent(input$show_snapshot_manager, {
+ invisible(self) |
| 104 | -! | +
- logger::log_debug("srv_snapshot_manager_panel@1 show_snapshot_manager button has been clicked.")
+ }, |
|
| 105 | -! | +
- showModal(+ |
|
| 106 | -! | +
- modalDialog(+ #' @description Sets content of this `TealSlicesBlock`. |
|
| 107 | -! | +
- ui_snapshot_manager(session$ns("module")),
+ #' Sets content as `YAML` text which represents a list generated from `teal_slices`. |
|
| 108 | -! | +
- class = "snapshot_manager_modal",+ #' The list displays limited number of fields from `teal_slice` objects, but this list is |
|
| 109 | -! | +
- size = "m",+ #' sufficient to conclude which filters were applied. |
|
| 110 | -! | +
- footer = NULL,+ #' When `selected` field in `teal_slice` object is a range, then it is displayed as a "min" |
|
| 111 | -! | +
- easyClose = TRUE+ #' |
|
| 112 |
- )+ #' |
||
| 113 |
- )+ #' @param content (`teal_slices`) object returned from [teal_slices()] function. |
||
| 114 |
- })+ #' @return `self`, invisibly. |
||
| 115 | -87x | +
- srv_snapshot_manager("module", slices_global = slices_global)
+ set_content = function(content) {
|
|
| 116 | -+ | 9x |
- })+ checkmate::assert_class(content, "teal_slices") |
| 117 | -+ | 8x |
- }+ if (length(content) != 0) {
|
| 118 | -+ | 6x |
-
+ states_list <- lapply(content, function(x) {
|
| 119 | -+ | 6x |
- #' @rdname module_snapshot_manager+ x_list <- shiny::isolate(as.list(x)) |
| 120 | -+ | 6x |
- ui_snapshot_manager <- function(id) {
+ if ( |
| 121 | -! | +6x |
- ns <- NS(id)+ inherits(x_list$choices, c("integer", "numeric", "Date", "POSIXct", "POSIXlt")) &&
|
| 122 | -! | +6x |
- tags$div(+ length(x_list$choices) == 2 && |
| 123 | -! | +6x |
- class = "manager_content",+ length(x_list$selected) == 2 |
| 124 | -! | +
- tags$div(+ ) {
|
|
| 125 | ! |
- class = "manager_table_row",+ x_list$range <- paste(x_list$selected, collapse = " - ") |
|
| 126 | ! |
- tags$span(tags$b("Snapshot manager")),
+ x_list["selected"] <- NULL |
|
| 127 | -! | +
- actionLink(ns("snapshot_add"), label = NULL, icon = icon("fas fa-camera"), title = "add snapshot"),
+ } |
|
| 128 | -! | +6x |
- actionLink(ns("snapshot_load"), label = NULL, icon = icon("fas fa-upload"), title = "upload snapshot"),
+ if (!is.null(x_list$arg)) {
|
| 129 | ! |
- actionLink(ns("snapshot_reset"), label = NULL, icon = icon("fas fa-undo"), title = "reset initial state"),
+ x_list$arg <- if (x_list$arg == "subset") "Genes" else "Samples" |
|
| 130 | -! | +
- NULL+ } |
|
| 131 |
- ),+ |
||
| 132 | -! | +6x |
- uiOutput(ns("snapshot_list"))
+ x_list <- x_list[ |
| 133 | -+ | 6x |
- )+ c("dataname", "varname", "experiment", "arg", "expr", "selected", "range", "keep_na", "keep_inf")
|
| 134 |
- }+ ] |
||
| 135 | -+ | 6x |
-
+ names(x_list) <- c( |
| 136 | -+ | 6x |
- #' @rdname module_snapshot_manager+ "Dataset name", "Variable name", "Experiment", "Filtering by", "Applied expression", |
| 137 | -+ | 6x |
- srv_snapshot_manager <- function(id, slices_global) {
+ "Selected Values", "Selected range", "Include NA values", "Include Inf values" |
| 138 | -87x | +
- checkmate::assert_character(id)+ ) |
|
| 140 | -87x | +6x |
- moduleServer(id, function(input, output, session) {
+ Filter(Negate(is.null), x_list) |
| 141 | -87x | +
- logger::log_debug("srv_snapshot_manager initializing")
+ }) |
|
| 143 | -+ | 6x |
- # Set up bookmarking callbacks ----+ if (requireNamespace("yaml", quietly = TRUE)) {
|
| 144 | -+ | 6x |
- # Register bookmark exclusions (all buttons and text fields).+ super$set_content(yaml::as.yaml(states_list)) |
| 145 | -87x | +
- setBookmarkExclude(c(+ } else {
|
|
| 146 | -87x | +! |
- "snapshot_add", "snapshot_load", "snapshot_reset",+ stop("yaml package is required to format the filter state list")
|
| 147 | -87x | +
- "snapshot_name_accept", "snaphot_file_accept",+ } |
|
| 148 | -87x | +
- "snapshot_name", "snapshot_file"+ } |
|
| 149 | -+ | 8x |
- ))+ private$teal_slices <- content |
| 150 | -+ | 8x |
- # Add snapshot history to bookmark.+ invisible(self) |
| 151 | -87x | +
- session$onBookmark(function(state) {
+ }, |
|
| 152 | -! | +
- logger::log_debug("srv_snapshot_manager@onBookmark: storing snapshot and bookmark history")
+ #' @description Create the `TealSlicesBlock` from a list. |
|
| 153 | -! | +
- state$values$snapshot_history <- snapshot_history() # isolate this?+ #' |
|
| 154 |
- })+ #' @param x (`named list`) with two fields `text` and `style`. |
||
| 155 |
-
+ #' Use the `get_available_styles` method to get all possible styles. |
||
| 156 | -87x | +
- ns <- session$ns+ #' |
|
| 157 |
-
+ #' @return `self`, invisibly. |
||
| 158 |
- # Track global filter states ----+ #' @examples |
||
| 159 | -87x | +
- snapshot_history <- reactiveVal({
+ #' TealSlicesBlock <- getFromNamespace("TealSlicesBlock", "teal")
|
|
| 160 |
- # Restore directly from bookmarked state, if applicable.+ #' block <- TealSlicesBlock$new() |
||
| 161 | -87x | +
- restoreValue(+ #' block$from_list(list(text = "sth", style = "default")) |
|
| 162 | -87x | +
- ns("snapshot_history"),
+ #' |
|
| 163 | -87x | +
- list("Initial application state" = shiny::isolate(as.list(slices_global$all_slices(), recursive = TRUE)))
+ from_list = function(x) {
|
|
| 164 | -+ | 1x |
- )+ checkmate::assert_list(x) |
| 165 | -+ | 1x |
- })+ checkmate::assert_names(names(x), must.include = c("text", "style"))
|
| 166 | -+ | 1x |
-
+ super$set_content(x$text) |
| 167 | -+ | 1x |
- # Snapshot current application state ----+ super$set_style(x$style) |
| 168 | -+ | 1x |
- # Name snaphsot.+ invisible(self) |
| 169 | -87x | +
- observeEvent(input$snapshot_add, {
+ }, |
|
| 170 | -! | +
- logger::log_debug("srv_snapshot_manager: snapshot_add button clicked")
+ #' @description Convert the `TealSlicesBlock` to a list. |
|
| 171 | -! | +
- showModal(+ #' |
|
| 172 | -! | +
- modalDialog(+ #' @return `named list` with a text and style. |
|
| 173 | -! | +
- textInput(ns("snapshot_name"), "Name the snapshot", width = "100%", placeholder = "Meaningful, unique name"),
+ #' @examples |
|
| 174 | -! | +
- footer = tagList(+ #' TealSlicesBlock <- getFromNamespace("TealSlicesBlock", "teal")
|
|
| 175 | -! | +
- actionButton(ns("snapshot_name_accept"), "Accept", icon = icon("far fa-thumbs-up")),
+ #' block <- TealSlicesBlock$new() |
|
| 176 | -! | +
- modalButton(label = "Cancel", icon = icon("far fa-thumbs-down"))
+ #' block$to_list() |
|
| 177 |
- ),+ #' |
||
| 178 | -! | +
- size = "s"+ to_list = function() {
|
|
| 179 | -+ | 2x |
- )+ content <- self$get_content() |
| 180 | -+ | 2x |
- )+ list( |
| 181 | -+ | 2x |
- })+ text = if (length(content)) content else "", |
| 182 | -+ | 2x |
- # Store snaphsot.+ style = self$get_style() |
| 183 | -87x | +
- observeEvent(input$snapshot_name_accept, {
+ ) |
|
| 184 | -! | +
- logger::log_debug("srv_snapshot_manager: snapshot_name_accept button clicked")
+ } |
|
| 185 | -! | +
- snapshot_name <- trimws(input$snapshot_name)+ ), |
|
| 186 | -! | +
- if (identical(snapshot_name, "")) {
+ private = list( |
|
| 187 | -! | +
- logger::log_debug("srv_snapshot_manager: snapshot name rejected")
+ style = "verbatim", |
|
| 188 | -! | +
- showNotification(+ teal_slices = NULL # teal_slices |
|
| 189 | -! | +
- "Please name the snapshot.",+ ) |
|
| 190 | -! | +
- type = "message"+ ) |
| 191 | +1 |
- )+ #' Send input validation messages to output |
||
| 192 | -! | +|||
| 2 | +
- updateTextInput(inputId = "snapshot_name", value = "", placeholder = "Meaningful, unique name")+ #' |
|||
| 193 | -! | +|||
| 3 | +
- } else if (is.element(make.names(snapshot_name), make.names(names(snapshot_history())))) {
+ #' Captures messages from `InputValidator` objects and collates them |
|||
| 194 | -! | +|||
| 4 | +
- logger::log_debug("srv_snapshot_manager: snapshot name rejected")
+ #' into one message passed to `validate`. |
|||
| 195 | -! | +|||
| 5 | +
- showNotification(+ #' |
|||
| 196 | -! | +|||
| 6 | +
- "This name is in conflict with other snapshot names. Please choose a different one.",+ #' `shiny::validate` is used to withhold rendering of an output element until |
|||
| 197 | -! | +|||
| 7 | +
- type = "message"+ #' certain conditions are met and to print a validation message in place |
|||
| 198 | +8 |
- )+ #' of the output element. |
||
| 199 | -! | +|||
| 9 | +
- updateTextInput(inputId = "snapshot_name", value = "", placeholder = "Meaningful, unique name")+ #' `shinyvalidate::InputValidator` allows to validate input elements |
|||
| 200 | +10 |
- } else {
+ #' and to display specific messages in their respective input widgets. |
||
| 201 | -! | +|||
| 11 | +
- logger::log_debug("srv_snapshot_manager: snapshot name accepted, adding snapshot")
+ #' `validate_inputs` provides a hybrid solution. |
|||
| 202 | -! | +|||
| 12 | +
- snapshot <- as.list(slices_global$all_slices(), recursive = TRUE)+ #' Given an `InputValidator` object, messages corresponding to inputs that fail validation |
|||
| 203 | -! | +|||
| 13 | ++ |
+ #' are extracted and placed in one validation message that is passed to a `validate`/`need` call.+ |
+ ||
| 14 | ++ |
+ #' This way the input `validator` messages are repeated in the output.+ |
+ ||
| 15 | ++ |
+ #'+ |
+ ||
| 16 | ++ |
+ #' The `...` argument accepts any number of `InputValidator` objects+ |
+ ||
| 17 | ++ |
+ #' or a nested list of such objects.+ |
+ ||
| 18 | ++ |
+ #' If `validators` are passed directly, all their messages are printed together+ |
+ ||
| 19 | ++ |
+ #' under one (optional) header message specified by `header`. If a list is passed,+ |
+ ||
| 20 | ++ |
+ #' messages are grouped by `validator`. The list's names are used as headers+ |
+ ||
| 21 | ++ |
+ #' for their respective message groups.+ |
+ ||
| 22 | ++ |
+ #' If neither of the nested list elements is named, a header message is taken from `header`.+ |
+ ||
| 23 | ++ |
+ #'+ |
+ ||
| 24 | ++ |
+ #' @param ... either any number of `InputValidator` objects+ |
+ ||
| 25 | ++ |
+ #' or an optionally named, possibly nested `list` of `InputValidator`+ |
+ ||
| 26 | ++ |
+ #' objects, see `Details`+ |
+ ||
| 27 | ++ |
+ #' @param header (`character(1)`) generic validation message; set to NULL to omit+ |
+ ||
| 28 | ++ |
+ #'+ |
+ ||
| 29 | +
- snapshot_update <- c(snapshot_history(), list(snapshot))+ #' @return |
|||
| 204 | -! | +|||
| 30 | +
- names(snapshot_update)[length(snapshot_update)] <- snapshot_name+ #' Returns NULL if the final validation call passes and a `shiny.silent.error` if it fails. |
|||
| 205 | -! | +|||
| 31 | +
- snapshot_history(snapshot_update)+ #' |
|||
| 206 | -! | +|||
| 32 | +
- removeModal()+ #' @seealso [`shinyvalidate::InputValidator`], [`shiny::validate`] |
|||
| 207 | +33 |
- # Reopen filter manager modal by clicking button in the main application.+ #' |
||
| 208 | -! | +|||
| 34 | +
- shinyjs::click(id = "teal-wunder_bar-show_snapshot_manager", asis = TRUE)+ #' @examplesIf require("shinyvalidate")
|
|||
| 209 | +35 |
- }+ #' library(shiny) |
||
| 210 | +36 |
- })+ #' library(shinyvalidate) |
||
| 211 | +37 |
-
+ #' |
||
| 212 | +38 |
- # Upload a snapshot file ----+ #' ui <- fluidPage( |
||
| 213 | +39 |
- # Select file.+ #' selectInput("method", "validation method", c("sequential", "combined", "grouped")),
|
||
| 214 | -87x | +|||
| 40 | +
- observeEvent(input$snapshot_load, {
+ #' sidebarLayout( |
|||
| 215 | -! | +|||
| 41 | +
- logger::log_debug("srv_snapshot_manager: snapshot_load button clicked")
+ #' sidebarPanel( |
|||
| 216 | -! | +|||
| 42 | +
- showModal(+ #' selectInput("letter", "select a letter:", c(letters[1:3], LETTERS[4:6])),
|
|||
| 217 | -! | +|||
| 43 | +
- modalDialog(+ #' selectInput("number", "select a number:", 1:6),
|
|||
| 218 | -! | +|||
| 44 | +
- fileInput(ns("snapshot_file"), "Choose snapshot file", accept = ".json", width = "100%"),
+ #' tags$br(), |
|||
| 219 | -! | +|||
| 45 | +
- textInput(+ #' selectInput("color", "select a color:",
|
|||
| 220 | -! | +|||
| 46 | +
- ns("snapshot_name"),
+ #' c("black", "indianred2", "springgreen2", "cornflowerblue"),
|
|||
| 221 | -! | +|||
| 47 | +
- "Name the snapshot (optional)",+ #' multiple = TRUE |
|||
| 222 | -! | +|||
| 48 | +
- width = "100%",+ #' ), |
|||
| 223 | -! | +|||
| 49 | +
- placeholder = "Meaningful, unique name"+ #' sliderInput("size", "select point size:",
|
|||
| 224 | +50 |
- ),+ #' min = 0.1, max = 4, value = 0.25 |
||
| 225 | -! | +|||
| 51 | +
- footer = tagList(+ #' ) |
|||
| 226 | -! | +|||
| 52 | +
- actionButton(ns("snaphot_file_accept"), "Accept", icon = icon("far fa-thumbs-up")),
+ #' ), |
|||
| 227 | -! | +|||
| 53 | +
- modalButton(label = "Cancel", icon = icon("far fa-thumbs-down"))
+ #' mainPanel(plotOutput("plot"))
|
|||
| 228 | +54 |
- )+ #' ) |
||
| 229 | +55 |
- )+ #' ) |
||
| 230 | +56 |
- )+ #' |
||
| 231 | +57 |
- })+ #' server <- function(input, output) {
|
||
| 232 | +58 |
- # Store new snapshot to list and restore filter states.+ #' # set up input validation |
||
| 233 | -87x | +|||
| 59 | +
- observeEvent(input$snaphot_file_accept, {
+ #' iv <- InputValidator$new() |
|||
| 234 | -! | +|||
| 60 | +
- logger::log_debug("srv_snapshot_manager: snapshot_file_accept button clicked")
+ #' iv$add_rule("letter", sv_in_set(LETTERS, "choose a capital letter"))
|
|||
| 235 | -! | +|||
| 61 | +
- snapshot_name <- trimws(input$snapshot_name)+ #' iv$add_rule("number", function(x) {
|
|||
| 236 | -! | +|||
| 62 | +
- if (identical(snapshot_name, "")) {
+ #' if (as.integer(x) %% 2L == 1L) "choose an even number" |
|||
| 237 | -! | +|||
| 63 | +
- logger::log_debug("srv_snapshot_manager: no snapshot name provided, naming after file")
+ #' }) |
|||
| 238 | -! | +|||
| 64 | +
- snapshot_name <- tools::file_path_sans_ext(input$snapshot_file$name)+ #' iv$enable() |
|||
| 239 | +65 |
- }+ #' # more input validation |
||
| 240 | -! | +|||
| 66 | +
- if (is.element(make.names(snapshot_name), make.names(names(snapshot_history())))) {
+ #' iv_par <- InputValidator$new() |
|||
| 241 | -! | +|||
| 67 | +
- logger::log_debug("srv_snapshot_manager: snapshot name rejected")
+ #' iv_par$add_rule("color", sv_required(message = "choose a color"))
|
|||
| 242 | -! | +|||
| 68 | +
- showNotification(+ #' iv_par$add_rule("color", function(x) {
|
|||
| 243 | -! | +|||
| 69 | +
- "This name is in conflict with other snapshot names. Please choose a different one.",+ #' if (length(x) > 1L) "choose only one color" |
|||
| 244 | -! | +|||
| 70 | +
- type = "message"+ #' }) |
|||
| 245 | +71 |
- )+ #' iv_par$add_rule( |
||
| 246 | -! | +|||
| 72 | +
- updateTextInput(inputId = "snapshot_name", value = "", placeholder = "Meaningful, unique name")+ #' "size", |
|||
| 247 | +73 |
- } else {
+ #' sv_between( |
||
| 248 | +74 |
- # Restore snapshot and verify app compatibility.+ #' left = 0.5, right = 3, |
||
| 249 | -! | +|||
| 75 | +
- logger::log_debug("srv_snapshot_manager: snapshot name accepted, loading snapshot")
+ #' message_fmt = "choose a value between {left} and {right}"
|
|||
| 250 | -! | +|||
| 76 | +
- snapshot_state <- try(slices_restore(input$snapshot_file$datapath))+ #' ) |
|||
| 251 | -! | +|||
| 77 | +
- if (!inherits(snapshot_state, "modules_teal_slices")) {
+ #' ) |
|||
| 252 | -! | +|||
| 78 | +
- logger::log_debug("srv_snapshot_manager: snapshot file corrupt")
+ #' iv_par$enable() |
|||
| 253 | -! | +|||
| 79 | +
- showNotification(+ #' |
|||
| 254 | -! | +|||
| 80 | +
- "File appears to be corrupt.",+ #' output$plot <- renderPlot({
|
|||
| 255 | -! | +|||
| 81 | +
- type = "error"+ #' # validate output |
|||
| 256 | +82 |
- )+ #' switch(input[["method"]], |
||
| 257 | -! | +|||
| 83 | +
- } else if (!identical(attr(snapshot_state, "app_id"), attr(slices_global$all_slices(), "app_id"))) {
+ #' "sequential" = {
|
|||
| 258 | -! | +|||
| 84 | +
- logger::log_debug("srv_snapshot_manager: snapshot not compatible with app")
+ #' validate_inputs(iv) |
|||
| 259 | -! | +|||
| 85 | +
- showNotification(+ #' validate_inputs(iv_par, header = "Set proper graphical parameters") |
|||
| 260 | -! | +|||
| 86 | +
- "This snapshot file is not compatible with the app and cannot be loaded.",+ #' }, |
|||
| 261 | -! | +|||
| 87 | +
- type = "warning"+ #' "combined" = validate_inputs(iv, iv_par), |
|||
| 262 | +88 |
- )+ #' "grouped" = validate_inputs(list( |
||
| 263 | +89 |
- } else {
+ #' "Some inputs require attention" = iv, |
||
| 264 | +90 |
- # Add to snapshot history.+ #' "Set proper graphical parameters" = iv_par |
||
| 265 | -! | +|||
| 91 | +
- logger::log_debug("srv_snapshot_manager: snapshot loaded, adding to history")
+ #' )) |
|||
| 266 | -! | +|||
| 92 | +
- snapshot <- as.list(slices_global$all_slices(), recursive = TRUE)+ #' ) |
|||
| 267 | -! | +|||
| 93 | +
- snapshot_update <- c(snapshot_history(), list(snapshot))+ #' |
|||
| 268 | -! | +|||
| 94 | +
- names(snapshot_update)[length(snapshot_update)] <- snapshot_name+ #' plot(faithful$eruptions ~ faithful$waiting, |
|||
| 269 | -! | +|||
| 95 | +
- snapshot_history(snapshot_update)+ #' las = 1, pch = 16, |
|||
| 270 | +96 |
- ### Begin simplified restore procedure. ###+ #' col = input[["color"]], cex = input[["size"]] |
||
| 271 | -! | +|||
| 97 | +
- logger::log_debug("srv_snapshot_manager: restoring snapshot")
+ #' ) |
|||
| 272 | -! | +|||
| 98 | +
- slices_global$slices_set(snapshot_state)+ #' }) |
|||
| 273 | -! | +|||
| 99 | +
- removeModal()+ #' } |
|||
| 274 | +100 |
- ### End simplified restore procedure. ###+ #' |
||
| 275 | +101 |
- }+ #' if (interactive()) {
|
||
| 276 | +102 |
- }+ #' shinyApp(ui, server) |
||
| 277 | +103 |
- })+ #' } |
||
| 278 | +104 |
- # Apply newly added snapshot.+ #' |
||
| 279 | +105 |
-
+ #' @export |
||
| 280 | +106 |
- # Restore initial state ----+ #' |
||
| 281 | -87x | +|||
| 107 | +
- observeEvent(input$snapshot_reset, {
+ validate_inputs <- function(..., header = "Some inputs require attention") {
|
|||
| 282 | -2x | +108 | +36x |
- logger::log_debug("srv_snapshot_manager: snapshot_reset button clicked, restoring snapshot")
+ dots <- list(...) |
| 283 | +109 | 2x |
- s <- "Initial application state"+ if (!is_validators(dots)) stop("validate_inputs accepts validators or a list thereof")
|
|
| 284 | +110 |
- ### Begin restore procedure. ###+ |
||
| 285 | -2x | +111 | +34x |
- snapshot <- snapshot_history()[[s]]+ messages <- extract_validator(dots, header) |
| 286 | -2x | +112 | +34x |
- snapshot_state <- as.teal_slices(snapshot)+ failings <- if (!any_names(dots)) {
|
| 287 | -2x | +113 | +29x |
- slices_global$slices_set(snapshot_state)+ add_header(messages, header) |
| 288 | -2x | +|||
| 114 | +
- removeModal()+ } else {
|
|||
| 289 | -+ | |||
| 115 | +5x |
- ### End restore procedure. ###+ unlist(messages) |
||
| 290 | +116 |
- })+ } |
||
| 291 | +117 | |||
| 292 | -+ | |||
| 118 | +34x |
- # Build snapshot table ----+ shiny::validate(shiny::need(is.null(failings), failings)) |
||
| 293 | +119 |
- # Create UI elements and server logic for the snapshot table.+ } |
||
| 294 | +120 |
- # Observers must be tracked to avoid duplication and excess reactivity.+ |
||
| 295 | +121 |
- # Remaining elements are tracked likewise for consistency and a slight speed margin.+ ### internal functions |
||
| 296 | -87x | +|||
| 122 | +
- observers <- reactiveValues()+ |
|||
| 297 | -87x | +|||
| 123 | +
- handlers <- reactiveValues()+ #' @noRd |
|||
| 298 | -87x | +|||
| 124 | +
- divs <- reactiveValues()+ #' @keywords internal |
|||
| 299 | +125 |
-
+ # recursive object type test |
||
| 300 | -87x | +|||
| 126 | +
- observeEvent(snapshot_history(), {
+ # returns logical of length 1 |
|||
| 301 | -77x | +|||
| 127 | +
- logger::log_debug("srv_snapshot_manager: snapshot history modified, updating snapshot list")
+ is_validators <- function(x) {
|
|||
| 302 | -77x | +128 | +118x |
- lapply(names(snapshot_history())[-1L], function(s) {
+ all(if (is.list(x)) unlist(lapply(x, is_validators)) else inherits(x, "InputValidator")) |
| 303 | -! | +|||
| 129 | +
- id_pickme <- sprintf("pickme_%s", make.names(s))
+ } |
|||
| 304 | -! | +|||
| 130 | +
- id_saveme <- sprintf("saveme_%s", make.names(s))
+
|
|||
| 305 | -! | +|||
| 131 | +
- id_rowme <- sprintf("rowme_%s", make.names(s))
+ #' @noRd |
|||
| 306 | +132 |
-
+ #' @keywords internal |
||
| 307 | +133 |
- # Observer for restoring snapshot.+ # test if an InputValidator object is enabled |
||
| 308 | -! | +|||
| 134 | +
- if (!is.element(id_pickme, names(observers))) {
+ # returns logical of length 1 |
|||
| 309 | -! | +|||
| 135 | +
- observers[[id_pickme]] <- observeEvent(input[[id_pickme]], {
+ # official method requested at https://github.com/rstudio/shinyvalidate/issues/64 |
|||
| 310 | +136 |
- ### Begin restore procedure. ###+ validator_enabled <- function(x) {
|
||
| 311 | -! | +|||
| 137 | +49x |
- snapshot <- snapshot_history()[[s]]+ x$.__enclos_env__$private$enabled |
||
| 312 | -! | +|||
| 138 | +
- snapshot_state <- as.teal_slices(snapshot)+ } |
|||
| 313 | +139 | |||
| 314 | -! | +|||
| 140 | +
- slices_global$slices_set(snapshot_state)+ #' Recursively extract messages from validator list |
|||
| 315 | -! | +|||
| 141 | +
- removeModal()+ #' @return A character vector or a list of character vectors, possibly nested and named. |
|||
| 316 | +142 |
- ### End restore procedure. ###+ #' @noRd |
||
| 317 | +143 |
- })+ #' @keywords internal |
||
| 318 | +144 |
- }+ extract_validator <- function(iv, header) {
|
||
| 319 | -+ | |||
| 145 | +113x |
- # Create handler for downloading snapshot.+ if (inherits(iv, "InputValidator")) {
|
||
| 320 | -! | +|||
| 146 | +49x |
- if (!is.element(id_saveme, names(handlers))) {
+ add_header(gather_messages(iv), header) |
||
| 321 | -! | +|||
| 147 | +
- output[[id_saveme]] <- downloadHandler(+ } else {
|
|||
| 322 | -! | +|||
| 148 | +58x |
- filename = function() {
+ if (is.null(names(iv))) names(iv) <- rep("", length(iv))
|
||
| 323 | -! | +|||
| 149 | +64x |
- sprintf("teal_snapshot_%s_%s.json", s, Sys.Date())
+ mapply(extract_validator, iv = iv, header = names(iv), SIMPLIFY = FALSE) |
||
| 324 | +150 |
- },+ } |
||
| 325 | -! | +|||
| 151 | +
- content = function(file) {
+ } |
|||
| 326 | -! | +|||
| 152 | +
- snapshot <- snapshot_history()[[s]]+ |
|||
| 327 | -! | +|||
| 153 | +
- snapshot_state <- as.teal_slices(snapshot)+ #' Collate failing messages from validator. |
|||
| 328 | -! | +|||
| 154 | +
- slices_store(tss = snapshot_state, file = file)+ #' @return `list` |
|||
| 329 | +155 |
- }+ #' @noRd |
||
| 330 | +156 |
- )+ #' @keywords internal |
||
| 331 | -! | +|||
| 157 | +
- handlers[[id_saveme]] <- id_saveme+ gather_messages <- function(iv) {
|
|||
| 332 | -+ | |||
| 158 | +49x |
- }+ if (validator_enabled(iv)) {
|
||
| 333 | -+ | |||
| 159 | +46x |
- # Create a row for the snapshot table.+ status <- iv$validate() |
||
| 334 | -! | +|||
| 160 | +46x |
- if (!is.element(id_rowme, names(divs))) {
+ failing_inputs <- Filter(Negate(is.null), status) |
||
| 335 | -! | +|||
| 161 | +46x |
- divs[[id_rowme]] <- tags$div(+ unique(lapply(failing_inputs, function(x) x[["message"]])) |
||
| 336 | -! | +|||
| 162 | +
- class = "manager_table_row",+ } else {
|
|||
| 337 | -! | +|||
| 163 | +3x |
- tags$span(tags$h5(s)),+ warning("Validator is disabled and will be omitted.")
|
||
| 338 | -! | +|||
| 164 | +3x |
- actionLink(inputId = ns(id_pickme), label = icon("far fa-circle-check"), title = "select"),
+ list() |
||
| 339 | -! | +|||
| 165 | +
- downloadLink(outputId = ns(id_saveme), label = icon("far fa-save"), title = "save to file")
+ } |
|||
| 340 | +166 |
- )+ } |
||
| 341 | +167 |
- }+ |
||
| 342 | +168 |
- })+ #' Add optional header to failing messages |
||
| 343 | +169 |
- })+ #' @noRd |
||
| 344 | +170 |
-
+ #' @keywords internal |
||
| 345 | +171 |
- # Create table to display list of snapshots and their actions.+ add_header <- function(messages, header = "") {
|
||
| 346 | -87x | +172 | +78x |
- output$snapshot_list <- renderUI({
+ ans <- unlist(messages) |
| 347 | -77x | +173 | +78x |
- rows <- rev(reactiveValuesToList(divs))+ if (length(ans) != 0L && isTRUE(nchar(header) > 0L)) {
|
| 348 | -77x | +174 | +31x |
- if (length(rows) == 0L) {
+ ans <- c(paste0(header, "\n"), ans, "\n") |
| 349 | -77x | +|||
| 175 | +
- tags$div(+ } |
|||
| 350 | -77x | +176 | +78x |
- class = "manager_placeholder",+ ans |
| 351 | -77x | +|||
| 177 | +
- "Snapshots will appear here."+ } |
|||
| 352 | +178 |
- )+ |
||
| 353 | +179 |
- } else {
+ #' Recursively check if the object contains a named list |
||
| 354 | -! | +|||
| 180 | +
- rows+ #' @noRd |
|||
| 355 | +181 |
- }+ #' @keywords internal |
||
| 356 | +182 |
- })+ any_names <- function(x) {
+ |
+ ||
| 183 | +103x | +
+ any(+ |
+ ||
| 184 | +103x | +
+ if (is.list(x)) {
+ |
+ ||
| 185 | +58x | +
+ if (!is.null(names(x)) && any(names(x) != "")) TRUE else unlist(lapply(x, any_names)) |
||
| 357 | +186 |
-
+ } else {
|
||
| 358 | -87x | +187 | +40x |
- snapshot_history+ FALSE |
| 359 | +188 |
- })+ } |
||
| 360 | +189 | ++ |
+ )+ |
+ |
| 190 |
}@@ -13657,1350 +12832,1791 @@ teal coverage - 60.11% |
| 1 |
- #' @title `TealReportCard`+ #' Execute and validate `teal_data_module` |
|||
| 2 |
- #' @description `r lifecycle::badge("experimental")`
+ #' |
|||
| 3 |
- #' Child class of [`teal.reporter::ReportCard`] that is used for `teal` specific applications.+ #' This is a low level module to handle `teal_data_module` execution and validation. |
|||
| 4 |
- #' In addition to the parent methods, it supports rendering `teal` specific elements such as+ #' [teal_transform_module()] inherits from [teal_data_module()] so it is handled by this module too. |
|||
| 5 |
- #' the source code, the encodings panel content and the filter panel content as part of the+ #' [srv_teal()] accepts various `data` objects and eventually they are all transformed to `reactive` |
|||
| 6 |
- #' meta data.+ #' [teal.data::teal_data()] which is a standard data class in whole `teal` framework. |
|||
| 7 |
- #' @export+ #' |
|||
| 8 |
- #'+ #' @section data validation: |
|||
| 9 |
- TealReportCard <- R6::R6Class( # nolint: object_name.+ #' |
|||
| 10 |
- classname = "TealReportCard",+ #' Executed [teal_data_module()] is validated and output is validated for consistency. |
|||
| 11 |
- inherit = teal.reporter::ReportCard,+ #' Output `data` is invalid if: |
|||
| 12 |
- public = list(+ #' 1. [teal_data_module()] is invalid if server doesn't return `reactive`. **Immediately crashes an app!** |
|||
| 13 |
- #' @description Appends the source code to the `content` meta data of this `TealReportCard`.+ #' 2. `reactive` throws a `shiny.error` - happens when module creating [teal.data::teal_data()] fails. |
|||
| 14 |
- #'+ #' 3. `reactive` returns `qenv.error` - happens when [teal.data::teal_data()] evaluates a failing code. |
|||
| 15 |
- #' @param src (`character(1)`) code as text.+ #' 4. `reactive` object doesn't return [teal.data::teal_data()]. |
|||
| 16 |
- #' @param ... any `rmarkdown` `R` chunk parameter and its value.+ #' 5. [teal.data::teal_data()] object lacks any `datanames` specified in the `modules` argument. |
|||
| 17 |
- #' But `eval` parameter is always set to `FALSE`.+ #'+ |
+ |||
| 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+ |
+ ||
| 20 | ++ |
+ #' resolved, the app will continue to run. `teal` guarantees that errors in data don't crash the app+ |
+ ||
| 21 | ++ |
+ #' (except error 1).+ |
+ ||
| 22 | ++ |
+ #'+ |
+ ||
| 23 | ++ |
+ #' @param id (`character(1)`) Module id+ |
+ ||
| 24 | ++ |
+ #' @param data (`reactive teal_data`)+ |
+ ||
| 25 | ++ |
+ #' @param data_module (`teal_data_module`)+ |
+ ||
| 26 | ++ |
+ #' @param modules (`teal_modules` or `teal_module`) For `datanames` validation purpose+ |
+ ||
| 27 | ++ |
+ #' @param validate_shiny_silent_error (`logical`) If `TRUE`, then `shiny.silent.error` is validated and+ |
+ ||
| 28 | ++ |
+ #' @param is_transform_failed (`reactiveValues`) contains `logical` flags named after each transformator.+ |
+ ||
| 29 | ++ |
+ #' Help to determine if any previous transformator failed, so that following transformators can be disabled+ |
+ ||
| 30 | ++ |
+ #' and display a generic failure message.+ |
+ ||
| 31 | ++ |
+ #'+ |
+ ||
| 32 | ++ |
+ #' @return `reactive` `teal_data`+ |
+ ||
| 33 | ++ |
+ #'+ |
+ ||
| 34 | ++ |
+ #' @rdname module_teal_data+ |
+ ||
| 35 | ++ |
+ #' @name module_teal_data+ |
+ ||
| 36 | ++ |
+ #' @keywords internal+ |
+ ||
| 37 | ++ |
+ NULL+ |
+ ||
| 38 | ++ | + + | +||
| 39 | ++ |
+ #' @rdname module_teal_data+ |
+ ||
| 40 | ++ |
+ #' @aliases ui_teal_data+ |
+ ||
| 41 | ++ |
+ #' @note+ |
+ ||
| 42 | ++ |
+ #' `ui_teal_data_module` was renamed from `ui_teal_data`.+ |
+ ||
| 43 | ++ |
+ ui_teal_data_module <- function(id, data_module = function(id) NULL) {
+ |
+ ||
| 44 | +! | +
+ checkmate::assert_string(id)+ |
+ ||
| 45 | +! | +
+ checkmate::assert_function(data_module, args = "id")+ |
+ ||
| 46 | +! | +
+ ns <- NS(id)+ |
+ ||
| 47 | ++ | + + | +||
| 48 | +! | +
+ shiny::tagList(+ |
+ ||
| 49 | +! | +
+ tags$div(id = ns("wrapper"), data_module(id = ns("data"))),
+ |
+ ||
| 50 | +! | +
+ ui_validate_reactive_teal_data(ns("validate"))
+ |
+ ||
| 51 | ++ |
+ )+ |
+ ||
| 52 | ++ |
+ }+ |
+ ||
| 53 | ++ | + + | +||
| 54 | ++ |
+ #' @rdname module_teal_data+ |
+ ||
| 55 | ++ |
+ #' @aliases srv_teal_data+ |
+ ||
| 56 | ++ |
+ #' @note+ |
+ ||
| 57 | ++ |
+ #' `srv_teal_data_module` was renamed from `srv_teal_data`.+ |
+ ||
| 58 | ++ |
+ srv_teal_data_module <- function(id,+ |
+ ||
| 59 | ++ |
+ data_module = function(id) NULL,+ |
+ ||
| 60 | ++ |
+ modules = NULL,+ |
+ ||
| 61 | ++ |
+ validate_shiny_silent_error = TRUE,+ |
+ ||
| 62 | ++ |
+ is_transform_failed = reactiveValues()) {
+ |
+ ||
| 63 | +! | +
+ checkmate::assert_string(id)+ |
+ ||
| 64 | +! | +
+ checkmate::assert_function(data_module, args = "id")+ |
+ ||
| 65 | +! | +
+ checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"), null.ok = TRUE)
+ |
+ ||
| 66 | +! | +
+ checkmate::assert_class(is_transform_failed, "reactivevalues")+ |
+ ||
| 67 | ++ | + + | +||
| 68 | +! | +
+ moduleServer(id, function(input, output, session) {
+ |
+ ||
| 69 | +! | +
+ logger::log_debug("srv_teal_data_module initializing.")
+ |
+ ||
| 70 | +! | +
+ is_transform_failed[[id]] <- FALSE+ |
+ ||
| 71 | +! | +
+ module_out <- data_module(id = "data")+ |
+ ||
| 72 | +! | +
+ try_module_out <- reactive(tryCatch(module_out(), error = function(e) e))+ |
+ ||
| 73 | +! | +
+ observeEvent(try_module_out(), {
+ |
+ ||
| 74 | +! | +
+ if (!inherits(try_module_out(), "teal_data")) {
+ |
+ ||
| 75 | +! | +
+ is_transform_failed[[id]] <- TRUE+ |
+ ||
| 76 | ++ |
+ } else {
+ |
+ ||
| 77 | +! | +
+ is_transform_failed[[id]] <- FALSE+ |
+ ||
| 78 | ++ |
+ }+ |
+ ||
| 79 | ++ |
+ })+ |
+ ||
| 80 | ++ | + + | +||
| 81 | +! | +
+ is_previous_failed <- reactive({
+ |
+ ||
| 82 | +! | +
+ idx_this <- which(names(is_transform_failed) == id)+ |
+ ||
| 83 | +! | +
+ is_transform_failed_list <- reactiveValuesToList(is_transform_failed)+ |
+ ||
| 84 | +! | +
+ idx_failures <- which(unlist(is_transform_failed_list))+ |
+ ||
| 85 | +! | +
+ any(idx_failures < idx_this)+ |
+ ||
| 86 | ++ |
+ })+ |
+ ||
| 87 | ++ | + | ||
| 18 | -+ | |||
| 88 | +! |
- #' @return Object of class `TealReportCard`, invisibly.+ observeEvent(is_previous_failed(), {
|
||
| 19 | -+ | |||
| 89 | +! |
- #' @examples+ if (is_previous_failed()) {
|
||
| 20 | -+ | |||
| 90 | +! |
- #' card <- TealReportCard$new()$append_src(+ shinyjs::disable("wrapper")
|
||
| 21 | +91 |
- #' "plot(iris)"+ } else {
|
||
| 22 | -+ | |||
| 92 | +! |
- #' )+ shinyjs::enable("wrapper")
|
||
| 23 | +93 |
- #' card$get_content()[[1]]$get_content()+ } |
||
| 24 | +94 |
- append_src = function(src, ...) {
+ }) |
||
| 25 | -4x | +|||
| 95 | +
- checkmate::assert_character(src, min.len = 0, max.len = 1)+ |
|||
| 26 | -4x | +|||
| 96 | +! |
- params <- list(...)+ srv_validate_reactive_teal_data( |
||
| 27 | -4x | +|||
| 97 | +! |
- params$eval <- FALSE+ "validate", |
||
| 28 | -4x | +|||
| 98 | +! |
- rblock <- RcodeBlock$new(src)+ data = try_module_out, |
||
| 29 | -4x | +|||
| 99 | +! |
- rblock$set_params(params)+ modules = modules, |
||
| 30 | -4x | +|||
| 100 | +! |
- self$append_content(rblock)+ validate_shiny_silent_error = validate_shiny_silent_error, |
||
| 31 | -4x | +|||
| 101 | +! |
- self$append_metadata("SRC", src)
+ hide_validation_error = is_previous_failed |
||
| 32 | -4x | +|||
| 102 | +
- invisible(self)+ ) |
|||
| 33 | +103 |
- },+ }) |
||
| 34 | +104 |
- #' @description Appends the filter state list to the `content` and `metadata` of this `TealReportCard`.+ } |
||
| 35 | +105 |
- #' If the filter state list has an attribute named `formatted`, it appends it to the card otherwise it uses+ |
||
| 36 | +106 |
- #' the default `yaml::as.yaml` to format the list.+ #' @rdname module_teal_data |
||
| 37 | +107 |
- #' If the filter state list is empty, nothing is appended to the `content`.+ ui_validate_reactive_teal_data <- function(id) {
|
||
| 38 | -+ | |||
| 108 | +! |
- #'+ ns <- NS(id) |
||
| 39 | -+ | |||
| 109 | +! |
- #' @param fs (`teal_slices`) object returned from [teal_slices()] function.+ tagList( |
||
| 40 | -+ | |||
| 110 | +! |
- #' @return `self`, invisibly.+ div( |
||
| 41 | -+ | |||
| 111 | +! |
- append_fs = function(fs) {
+ id = ns("validate_messages"),
|
||
| 42 | -5x | +|||
| 112 | +! |
- checkmate::assert_class(fs, "teal_slices")+ class = "teal_validated", |
||
| 43 | -4x | +|||
| 113 | +! |
- self$append_text("Filter State", "header3")
+ ui_validate_error(ns("silent_error")),
|
||
| 44 | -4x | +|||
| 114 | +! |
- if (length(fs)) {
+ ui_check_class_teal_data(ns("class_teal_data")),
|
||
| 45 | -3x | +|||
| 115 | +! |
- self$append_content(TealSlicesBlock$new(fs))+ ui_check_module_datanames(ns("shiny_warnings"))
|
||
| 46 | +116 |
- } else {
+ ), |
||
| 47 | -1x | +|||
| 117 | +! |
- self$append_text("No filters specified.")
+ div( |
||
| 48 | -+ | |||
| 118 | +! |
- }+ class = "teal_validated", |
||
| 49 | -4x | +|||
| 119 | +! |
- invisible(self)+ uiOutput(ns("previous_failed"))
|
||
| 50 | +120 |
- },+ ) |
||
| 51 | +121 |
- #' @description Appends the encodings list to the `content` and `metadata` of this `TealReportCard`.+ ) |
||
| 52 | +122 |
- #'+ } |
||
| 53 | +123 |
- #' @param encodings (`list`) list of encodings selections of the `teal` app.+ |
||
| 54 | +124 |
- #' @return `self`, invisibly.+ #' @rdname module_teal_data |
||
| 55 | +125 |
- #' @examples+ srv_validate_reactive_teal_data <- function(id, # nolint: object_length |
||
| 56 | +126 |
- #' card <- TealReportCard$new()$append_encodings(list(variable1 = "X"))+ data, |
||
| 57 | +127 |
- #' card$get_content()[[1]]$get_content()+ modules = NULL, |
||
| 58 | +128 |
- #'+ validate_shiny_silent_error = FALSE, |
||
| 59 | +129 |
- append_encodings = function(encodings) {
- |
- ||
| 60 | -4x | -
- checkmate::assert_list(encodings)- |
- ||
| 61 | -4x | -
- self$append_text("Selected Options", "header3")
- |
- ||
| 62 | -4x | -
- if (requireNamespace("yaml", quietly = TRUE)) {
+ hide_validation_error = reactive(FALSE)) {
|
||
| 63 | -4x | +|||
| 130 | +! |
- self$append_text(yaml::as.yaml(encodings, handlers = list(+ checkmate::assert_string(id) |
||
| 64 | -4x | +|||
| 131 | +! |
- POSIXct = function(x) format(x, "%Y-%m-%d"),+ checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"), null.ok = TRUE)
|
||
| 65 | -4x | +|||
| 132 | +! |
- POSIXlt = function(x) format(x, "%Y-%m-%d"),+ checkmate::assert_flag(validate_shiny_silent_error) |
||
| 66 | -4x | +|||
| 133 | +
- Date = function(x) format(x, "%Y-%m-%d")+ |
|||
| 67 | -4x | +|||
| 134 | +! |
- )), "verbatim")+ moduleServer(id, function(input, output, session) {
|
||
| 68 | +135 |
- } else {
+ # there is an empty reactive cycle on `init` and `data` has `shiny.silent.error` class |
||
| 69 | +136 | ! |
- stop("yaml package is required to format the encodings list")
+ srv_validate_error("silent_error", data, validate_shiny_silent_error)
|
|
| 70 | -+ | |||
| 137 | +! |
- }+ srv_check_class_teal_data("class_teal_data", data)
|
||
| 71 | -4x | +|||
| 138 | +! |
- self$append_metadata("Encodings", encodings)
+ srv_check_module_datanames("shiny_warnings", data, modules)
|
||
| 72 | -4x | +|||
| 139 | +! |
- invisible(self)+ output$previous_failed <- renderUI({
|
||
| 73 | -+ | |||
| 140 | +! |
- }+ if (hide_validation_error()) {
|
||
| 74 | -+ | |||
| 141 | +! |
- ),+ shinyjs::hide("validate_messages")
|
||
| 75 | -+ | |||
| 142 | +! |
- private = list(+ tags$div("One of previous transformators failed. Please check its inputs.", class = "teal-output-warning")
|
||
| 76 | +143 |
- dispatch_block = function(block_class) {
+ } else {
|
||
| 77 | +144 | ! |
- eval(str2lang(block_class))+ shinyjs::show("validate_messages")
|
|
| 78 | -+ | |||
| 145 | +! |
- }+ NULL |
||
| 79 | +146 |
- )+ } |
||
| 80 | +147 |
- )+ }) |
||
| 81 | +148 | |||
| 82 | -+ | |||
| 149 | +! |
- #' @title `TealSlicesBlock`+ .trigger_on_success(data) |
||
| 83 | +150 |
- #' @docType class+ }) |
||
| 84 | +151 |
- #' @description+ } |
||
| 85 | +152 |
- #' Specialized `TealSlicesBlock` block for managing filter panel content in reports.+ |
||
| 86 | +153 |
#' @keywords internal |
||
| 87 | -- |
- TealSlicesBlock <- R6::R6Class( # nolint: object_name_linter.- |
- ||
| 88 | +154 |
- classname = "TealSlicesBlock",+ ui_validate_error <- function(id) {
|
||
| 89 | -+ | |||
| 155 | +116x |
- inherit = teal.reporter:::TextBlock,+ ns <- NS(id) |
||
| 90 | -+ | |||
| 156 | +116x |
- public = list(+ uiOutput(ns("message"))
|
||
| 91 | +157 |
- #' @description Returns a `TealSlicesBlock` object.+ } |
||
| 92 | +158 |
- #'+ |
||
| 93 | +159 |
- #' @details Returns a `TealSlicesBlock` object with no content and no parameters.+ #' @keywords internal |
||
| 94 | +160 |
- #'+ srv_validate_error <- function(id, data, validate_shiny_silent_error) {
|
||
| 95 | -+ | |||
| 161 | +113x |
- #' @param content (`teal_slices`) object returned from [teal_slices()] function.+ checkmate::assert_string(id) |
||
| 96 | -+ | |||
| 162 | +113x |
- #' @param style (`character(1)`) string specifying style to apply.+ checkmate::assert_flag(validate_shiny_silent_error) |
||
| 97 | -+ | |||
| 163 | +113x |
- #'+ moduleServer(id, function(input, output, session) {
|
||
| 98 | -+ | |||
| 164 | +113x |
- #' @return Object of class `TealSlicesBlock`, invisibly.+ output$message <- renderUI({
|
||
| 99 | -+ | |||
| 165 | +112x |
- #'+ is_shiny_silent_error <- inherits(data(), "shiny.silent.error") && identical(data()$message, "") |
||
| 100 | -+ | |||
| 166 | +112x |
- initialize = function(content = teal_slices(), style = "verbatim") {
+ if (inherits(data(), "qenv.error")) {
|
||
| 101 | -9x | +167 | +2x |
- self$set_content(content)+ validate( |
| 102 | -8x | +168 | +2x |
- self$set_style(style)+ need( |
| 103 | -8x | +169 | +2x |
- invisible(self)+ FALSE, |
| 104 | -+ | |||
| 170 | +2x |
- },+ paste( |
||
| 105 | -+ | |||
| 171 | +2x |
-
+ "Error when executing the `data` module:", |
||
| 106 | -+ | |||
| 172 | +2x |
- #' @description Sets content of this `TealSlicesBlock`.+ strip_style(paste(data()$message, collapse = "\n")), |
||
| 107 | -+ | |||
| 173 | +2x |
- #' Sets content as `YAML` text which represents a list generated from `teal_slices`.+ "\nCheck your inputs or contact app developer if error persists.", |
||
| 108 | -+ | |||
| 174 | +2x |
- #' The list displays limited number of fields from `teal_slice` objects, but this list is+ collapse = "\n" |
||
| 109 | +175 |
- #' sufficient to conclude which filters were applied.+ ) |
||
| 110 | +176 |
- #' When `selected` field in `teal_slice` object is a range, then it is displayed as a "min"+ ) |
||
| 111 | +177 |
- #'+ ) |
||
| 112 | -+ | |||
| 178 | +110x |
- #'+ } else if (inherits(data(), "error")) {
|
||
| 113 | -+ | |||
| 179 | +11x |
- #' @param content (`teal_slices`) object returned from [teal_slices()] function.+ if (is_shiny_silent_error && !validate_shiny_silent_error) {
|
||
| 114 | -+ | |||
| 180 | +4x |
- #' @return `self`, invisibly.+ return(NULL) |
||
| 115 | +181 |
- set_content = function(content) {
- |
- ||
| 116 | -9x | -
- checkmate::assert_class(content, "teal_slices")+ } |
||
| 117 | -8x | +182 | +7x |
- if (length(content) != 0) {
+ validate( |
| 118 | -6x | +183 | +7x |
- states_list <- lapply(content, function(x) {
+ need( |
| 119 | -6x | +184 | +7x |
- x_list <- shiny::isolate(as.list(x))+ FALSE, |
| 120 | -6x | +185 | +7x |
- if (+ sprintf( |
| 121 | -6x | +186 | +7x |
- inherits(x_list$choices, c("integer", "numeric", "Date", "POSIXct", "POSIXlt")) &&
+ "Shiny error when executing the `data` module.\n%s\n%s", |
| 122 | -6x | +187 | +7x |
- length(x_list$choices) == 2 &&+ data()$message, |
| 123 | -6x | +188 | +7x |
- length(x_list$selected) == 2+ "Check your inputs or contact app developer if error persists." |
| 124 | +189 |
- ) {
+ ) |
||
| 125 | -! | +|||
| 190 | +
- x_list$range <- paste(x_list$selected, collapse = " - ")+ ) |
|||
| 126 | -! | +|||
| 191 | +
- x_list["selected"] <- NULL+ ) |
|||
| 127 | +192 |
- }+ } |
||
| 128 | -6x | +|||
| 193 | +
- if (!is.null(x_list$arg)) {
+ }) |
|||
| 129 | -! | +|||
| 194 | +
- x_list$arg <- if (x_list$arg == "subset") "Genes" else "Samples"+ }) |
|||
| 130 | +195 |
- }+ } |
||
| 131 | +196 | |||
| 132 | -6x | -
- x_list <- x_list[- |
- ||
| 133 | -6x | +|||
| 197 | +
- c("dataname", "varname", "experiment", "arg", "expr", "selected", "range", "keep_na", "keep_inf")
+
|
|||
| 134 | +198 |
- ]+ #' @keywords internal |
||
| 135 | -6x | +|||
| 199 | +
- names(x_list) <- c(+ ui_check_class_teal_data <- function(id) {
|
|||
| 136 | -6x | +200 | +116x |
- "Dataset name", "Variable name", "Experiment", "Filtering by", "Applied expression",+ ns <- NS(id) |
| 137 | -6x | +201 | +116x |
- "Selected Values", "Selected range", "Include NA values", "Include Inf values"+ uiOutput(ns("message"))
|
| 138 | +202 |
- )+ } |
||
| 139 | +203 | |||
| 140 | -6x | -
- Filter(Negate(is.null), x_list)- |
- ||
| 141 | +204 |
- })+ #' @keywords internal |
||
| 142 | +205 |
-
+ srv_check_class_teal_data <- function(id, data) {
|
||
| 143 | -6x | +206 | +113x |
- if (requireNamespace("yaml", quietly = TRUE)) {
+ checkmate::assert_string(id) |
| 144 | -6x | -
- super$set_content(yaml::as.yaml(states_list))- |
- ||
| 145 | -+ | 207 | +113x |
- } else {
+ moduleServer(id, function(input, output, session) {
|
| 146 | -! | +|||
| 208 | +113x |
- stop("yaml package is required to format the filter state list")
+ output$message <- renderUI({
|
||
| 147 | -+ | |||
| 209 | +112x |
- }+ validate( |
||
| 148 | -+ | |||
| 210 | +112x |
- }+ need( |
||
| 149 | -8x | +211 | +112x |
- private$teal_slices <- content+ inherits(data(), c("teal_data", "error")),
|
| 150 | -8x | +212 | +112x |
- invisible(self)+ "Did not receive `teal_data` object. Cannot proceed further." |
| 151 | +213 |
- },+ ) |
||
| 152 | +214 |
- #' @description Create the `TealSlicesBlock` from a list.+ ) |
||
| 153 | +215 |
- #'+ }) |
||
| 154 | +216 |
- #' @param x (`named list`) with two fields `text` and `style`.+ }) |
||
| 155 | +217 |
- #' Use the `get_available_styles` method to get all possible styles.+ } |
||
| 156 | +218 |
- #'+ |
||
| 157 | +219 |
- #' @return `self`, invisibly.+ #' @keywords internal |
||
| 158 | +220 |
- #' @examples+ ui_check_module_datanames <- function(id) {
|
||
| 159 | -+ | |||
| 221 | +116x |
- #' TealSlicesBlock <- getFromNamespace("TealSlicesBlock", "teal")
+ ns <- NS(id)+ |
+ ||
| 222 | +116x | +
+ uiOutput(NS(id, "message")) |
||
| 160 | +223 |
- #' block <- TealSlicesBlock$new()+ } |
||
| 161 | +224 |
- #' block$from_list(list(text = "sth", style = "default"))+ |
||
| 162 | +225 |
- #'+ #' @keywords internal |
||
| 163 | +226 |
- from_list = function(x) {
+ srv_check_module_datanames <- function(id, data, modules) {
|
||
| 164 | -1x | +227 | +193x |
- checkmate::assert_list(x)+ checkmate::assert_string(id) |
| 165 | -1x | +228 | +193x |
- checkmate::assert_names(names(x), must.include = c("text", "style"))
+ moduleServer(id, function(input, output, session) {
|
| 166 | -1x | +229 | +193x |
- super$set_content(x$text)+ output$message <- renderUI({
|
| 167 | -1x | +230 | +196x |
- super$set_style(x$style)+ if (inherits(data(), "teal_data")) {
|
| 168 | -1x | +231 | +179x |
- invisible(self)+ is_modules_ok <- check_modules_datanames_html( |
| 169 | -+ | |||
| 232 | +179x |
- },+ modules = modules, datanames = names(data()) |
||
| 170 | +233 |
- #' @description Convert the `TealSlicesBlock` to a list.+ ) |
||
| 171 | -+ | |||
| 234 | +179x |
- #'+ if (!isTRUE(is_modules_ok)) {
|
||
| 172 | -+ | |||
| 235 | +19x |
- #' @return `named list` with a text and style.+ tags$div(is_modules_ok, class = "teal-output-warning") |
||
| 173 | +236 |
- #' @examples+ } |
||
| 174 | +237 |
- #' TealSlicesBlock <- getFromNamespace("TealSlicesBlock", "teal")
+ } |
||
| 175 | +238 |
- #' block <- TealSlicesBlock$new()+ }) |
||
| 176 | +239 |
- #' block$to_list()+ }) |
||
| 177 | +240 |
- #'+ } |
||
| 178 | +241 |
- to_list = function() {
+
|
||
| 179 | -2x | +|||
| 242 | +
- content <- self$get_content()+ .trigger_on_success <- function(data) {
|
|||
| 180 | -2x | +243 | +113x |
- list(+ out <- reactiveVal(NULL) |
| 181 | -2x | +244 | +113x |
- text = if (length(content)) content else "",+ observeEvent(data(), {
|
| 182 | -2x | +245 | +112x |
- style = self$get_style()+ if (inherits(data(), "teal_data")) {
|
| 183 | -+ | |||
| 246 | +97x |
- )+ if (!identical(data(), out())) {
|
||
| 184 | -+ | |||
| 247 | +97x |
- }+ out(data()) |
||
| 185 | +248 |
- ),+ } |
||
| 186 | +249 |
- private = list(+ } |
||
| 187 | +250 |
- style = "verbatim",+ }) |
||
| 188 | +251 |
- teal_slices = NULL # teal_slices+ |
||
| 189 | -+ | |||
| 252 | +113x |
- )+ out |
||
| 190 | +253 |
- )+ } |
| 1 |
- #' An example `teal` module+ #' Data module for `teal` transformations and output customization |
||
| 3 |
- #' `r lifecycle::badge("experimental")`
+ #' @description |
||
| 4 |
- #'+ #' `r lifecycle::badge("experimental")`
|
||
| 5 |
- #' This module creates an object called `object` that can be modified with decorators.+ #' |
||
| 6 |
- #' The `object` is determined by what's selected in `Choose a dataset` input in UI.+ #' `teal_transform_module` provides a `shiny` module that enables data transformations within a `teal` application |
||
| 7 |
- #' The object can be anything that can be handled by `renderPrint()`.+ #' and allows for customization of outputs generated by modules. |
||
| 8 |
- #' See the `vignette("decorate-modules-output", package = "teal")` or [`teal_transform_module`]
+ #' |
||
| 9 |
- #' to read more about decorators.+ #' # Transforming Module Inputs in `teal` |
||
| 11 |
- #' @inheritParams teal_modules+ #' Data transformations occur after data has been filtered in `teal`. |
||
| 12 |
- #' @param decorators `r lifecycle::badge("experimental")` (`list` of `teal_transform_module` or `NULL`) optional,
+ #' The transformed data is then passed to the `server` of [`teal_module()`] and managed by `teal`'s internal processes. |
||
| 13 |
- #' if not `NULL`, decorator for tables or plots included in the module.+ #' The primary advantage of `teal_transform_module` over custom modules is in its error handling, where all warnings and |
||
| 14 |
- #'+ #' errors are managed by `teal`, allowing developers to focus on transformation logic. |
||
| 15 |
- #' @return A `teal` module which can be included in the `modules` argument to [init()].+ #' |
||
| 16 |
- #' @examples+ #' For more details, see the vignette: `vignette("data-transform-as-shiny-module", package = "teal")`.
|
||
| 17 |
- #' app <- init(+ #' |
||
| 18 |
- #' data = teal_data(IRIS = iris, MTCARS = mtcars),+ #' # Customizing Module Outputs |
||
| 19 |
- #' modules = example_module()+ #' |
||
| 20 |
- #' )+ #' `teal_transform_module` also allows developers to modify any object created within [`teal.data::teal_data`]. |
||
| 21 |
- #' if (interactive()) {
+ #' This means you can use it to customize not only datasets but also tables, listings, and graphs. |
||
| 22 |
- #' shinyApp(app$ui, app$server)+ #' Some [`teal_modules`] permit developers to inject custom `shiny` modules to enhance displayed outputs. |
||
| 23 |
- #' }+ #' To manage these `decorators` within your module, use [`ui_transform_teal_data()`] and [`srv_transform_teal_data()`]. |
||
| 24 |
- #' @export+ #' (For further guidance on managing decorators, refer to `ui_args` and `srv_args` in the vignette documentation.) |
||
| 25 |
- example_module <- function(label = "example teal module",+ #' |
||
| 26 |
- datanames = "all",+ #' See the vignette `vignette("decorate-modules-output", package = "teal")` for additional examples.
|
||
| 27 |
- transformators = list(),+ #' |
||
| 28 |
- decorators = NULL) {
+ #' # `server` as a language |
||
| 29 | -43x | -
- checkmate::assert_string(label)- |
- |
| 30 | -43x | +
- checkmate::assert_list(decorators, "teal_transform_module", null.ok = TRUE)+ #' |
|
| 31 | +30 | - - | -|
| 32 | -43x | -
- ans <- module(- |
- |
| 33 | -43x | -
- label,- |
- |
| 34 | -43x | -
- server = function(id, data, decorators) {
- |
- |
| 35 | -5x | -
- checkmate::assert_class(isolate(data()), "teal_data")- |
- |
| 36 | -5x | -
- moduleServer(id, function(input, output, session) {
- |
- |
| 37 | -5x | -
- datanames_rv <- reactive(names(req(data())))- |
- |
| 38 | -5x | -
- observeEvent(datanames_rv(), {
- |
- |
| 39 | -5x | -
- selected <- input$dataname- |
- |
| 40 | -5x | -
- if (identical(selected, "")) {
- |
- |
| 41 | -! | -
- selected <- restoreInput(session$ns("dataname"), NULL)
- |
- |
| 42 | -5x | -
- } else if (isFALSE(selected %in% datanames_rv())) {
- |
- |
| 43 | -! | -
- selected <- datanames_rv()[1]+ #' The `server` function in `teal_transform_module` must return a reactive [`teal.data::teal_data`] object. |
|
| 44 | +31 |
- }- |
- |
| 45 | -5x | -
- updateSelectInput(- |
- |
| 46 | -5x | -
- session = session,- |
- |
| 47 | -5x | -
- inputId = "dataname",- |
- |
| 48 | -5x | -
- choices = datanames_rv(),- |
- |
| 49 | -5x | -
- selected = selected+ #' For simple transformations without complex reactivity, the `server` function might look like this:s |
|
| 50 | +32 |
- )+ #' |
|
| 51 | +33 |
- })+ #' ``` |
|
| 52 | +34 | - - | -|
| 53 | -5x | -
- table_data <- reactive({
- |
- |
| 54 | -8x | -
- req(input$dataname)- |
- |
| 55 | -3x | -
- within(data(),+ #' function(id, data) {
|
|
| 56 | +35 |
- {
- |
- |
| 57 | -3x | -
- object <- dataname+ #' moduleServer(id, function(input, output, session) {
|
|
| 58 | +36 |
- },- |
- |
| 59 | -3x | -
- dataname = as.name(input$dataname)+ #' reactive({
|
|
| 60 | +37 |
- )+ #' within( |
|
| 61 | +38 |
- })+ #' data(), |
|
| 62 | +39 | - - | -|
| 63 | -5x | -
- table_data_decorated_no_print <- srv_transform_teal_data(- |
- |
| 64 | -5x | -
- "decorate",- |
- |
| 65 | -5x | -
- data = table_data,- |
- |
| 66 | -5x | -
- transformators = decorators+ #' expr = x <- subset(x, col == level), |
|
| 67 | +40 |
- )- |
- |
| 68 | -5x | -
- table_data_decorated <- reactive(within(req(table_data_decorated_no_print()), expr = object))+ #' level = input$level |
|
| 69 | +41 | - - | -|
| 70 | -5x | -
- output$text <- renderPrint({
- |
- |
| 71 | -9x | -
- req(table_data()) # Ensure original errors from module are displayed- |
- |
| 72 | -4x | -
- table_data_decorated()[["object"]]+ #' ) |
|
| 73 | +42 |
- })+ #' }) |
|
| 74 | +43 | - - | -|
| 75 | -5x | -
- teal.widgets::verbatim_popup_srv(- |
- |
| 76 | -5x | -
- id = "rcode",- |
- |
| 77 | -5x | -
- verbatim_content = reactive(teal.code::get_code(req(table_data_decorated()))),- |
- |
| 78 | -5x | -
- title = "Example Code"+ #' }) |
|
| 79 | +44 |
- )+ #' } |
|
| 80 | +45 | - - | -|
| 81 | -5x | -
- table_data_decorated+ #' ``` |
|
| 82 | +46 |
- })+ #' |
|
| 83 | +47 |
- },- |
- |
| 84 | -43x | -
- ui = function(id, decorators) {
- |
- |
| 85 | -! | -
- ns <- NS(id)- |
- |
| 86 | -! | -
- teal.widgets::standard_layout(- |
- |
| 87 | -! | -
- output = verbatimTextOutput(ns("text")),
- |
- |
| 88 | -! | -
- encoding = tags$div(- |
- |
| 89 | -! | -
- selectInput(ns("dataname"), "Choose a dataset", choices = NULL),
- |
- |
| 90 | -! | -
- ui_transform_teal_data(ns("decorate"), transformators = decorators),
- |
- |
| 91 | -! | -
- teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
+ #' The example above can be simplified using `make_teal_transform_server`, where `level` is automatically matched to the |
|
| 92 | +48 |
- )+ #' corresponding `input` parameter: |
|
| 93 | +49 |
- )+ #' |
|
| 94 | +50 |
- },- |
- |
| 95 | -43x | -
- ui_args = list(decorators = decorators),- |
- |
| 96 | -43x | -
- server_args = list(decorators = decorators),- |
- |
| 97 | -43x | -
- datanames = datanames,- |
- |
| 98 | -43x | -
- transformators = transformators+ #' ``` |
|
| 99 | +51 |
- )- |
- |
| 100 | -43x | -
- attr(ans, "teal_bookmarkable") <- TRUE- |
- |
| 101 | -43x | -
- ans+ #' make_teal_transform_server(expr = expression(x <- subset(x, col == level))) |
|
| 102 | +52 |
- }+ #' ``` |
| 1 | +53 |
- #' Filter settings for `teal` applications+ #' @inheritParams teal_data_module |
||
| 2 | +54 |
- #'+ #' @param server (`function(id, data)` or `expression`) |
||
| 3 | +55 |
- #' Specify initial filter states and filtering settings for a `teal` app.+ #' A `shiny` module server function that takes `id` and `data` as arguments, where `id` is the module id and `data` |
||
| 4 | +56 |
- #'+ #' is the reactive `teal_data` input. The `server` function must return a reactive expression containing a `teal_data` |
||
| 5 | +57 |
- #' Produces a `teal_slices` object.+ #' object. For simplified syntax, use [`make_teal_transform_server()`]. |
||
| 6 | +58 |
- #' The `teal_slice` components will specify filter states that will be active when the app starts.+ #' @param datanames (`character`) |
||
| 7 | +59 |
- #' Attributes (created with the named arguments) will configure the way the app applies filters.+ #' Specifies the names of datasets relevant to the module. Only filters for the specified `datanames` will be displayed |
||
| 8 | +60 |
- #' See argument descriptions for details.+ #' in the filter panel. The keyword `"all"` can be used to display filters for all datasets. `datanames` are |
||
| 9 | +61 |
- #'+ #' automatically appended to the [`modules()`] `datanames`. |
||
| 10 | +62 |
- #' @inheritParams teal.slice::teal_slices+ #' |
||
| 11 | +63 |
#' |
||
| 12 | +64 |
- #' @param module_specific (`logical(1)`) optional,+ #' @examples |
||
| 13 | +65 |
- #' - `FALSE` (default) when one filter panel applied to all modules.+ #' data_transformators <- list( |
||
| 14 | +66 |
- #' All filters will be shared by all modules.+ #' teal_transform_module( |
||
| 15 | +67 |
- #' - `TRUE` when filter panel module-specific.+ #' label = "Static transformator for iris", |
||
| 16 | +68 |
- #' Modules can have different set of filters specified - see `mapping` argument.+ #' datanames = "iris", |
||
| 17 | +69 |
- #' @param mapping `r lifecycle::badge("experimental")`
+ #' server = function(id, data) {
|
||
| 18 | +70 |
- #' _This is a new feature. Do kindly share your opinions on+ #' moduleServer(id, function(input, output, session) {
|
||
| 19 | +71 |
- #' [`teal`'s GitHub repository](https://github.com/insightsengineering/teal/)._+ #' reactive({
|
||
| 20 | +72 |
- #'+ #' within(data(), {
|
||
| 21 | +73 |
- #' (named `list`) specifies which filters will be active in which modules on app start.+ #' iris <- head(iris, 5) |
||
| 22 | +74 |
- #' Elements should contain character vector of `teal_slice` `id`s (see [`teal.slice::teal_slice`]).+ #' }) |
||
| 23 | +75 |
- #' Names of the list should correspond to `teal_module` `label` set in [module()] function.+ #' }) |
||
| 24 | +76 |
- #' - `id`s listed under `"global_filters` will be active in all modules.+ #' }) |
||
| 25 | +77 |
- #' - If missing, all filters will be applied to all modules.+ #' } |
||
| 26 | +78 |
- #' - If empty list, all filters will be available to all modules but will start inactive.+ #' ), |
||
| 27 | +79 |
- #' - If `module_specific` is `FALSE`, only `global_filters` will be active on start.+ #' teal_transform_module( |
||
| 28 | +80 |
- #' @param app_id (`character(1)`)+ #' label = "Interactive transformator for iris", |
||
| 29 | +81 |
- #' For internal use only, do not set manually.+ #' datanames = "iris", |
||
| 30 | +82 |
- #' Added by `init` so that a `teal_slices` can be matched to the app in which it was used.+ #' ui = function(id) {
|
||
| 31 | +83 |
- #' Used for verifying snapshots uploaded from file. See `snapshot`.+ #' ns <- NS(id) |
||
| 32 | +84 |
- #'+ #' tags$div( |
||
| 33 | +85 |
- #' @param x (`list`) of lists to convert to `teal_slices`+ #' numericInput(ns("n_cols"), "Show n columns", value = 5, min = 1, max = 5, step = 1)
|
||
| 34 | +86 |
- #'+ #' ) |
||
| 35 | +87 |
- #' @return+ #' }, |
||
| 36 | +88 |
- #' A `teal_slices` object.+ #' server = function(id, data) {
|
||
| 37 | +89 |
- #'+ #' moduleServer(id, function(input, output, session) {
|
||
| 38 | +90 |
- #' @seealso [`teal.slice::teal_slices`], [`teal.slice::teal_slice`], [slices_store()]+ #' reactive({
|
||
| 39 | +91 |
- #'+ #' within(data(), |
||
| 40 | +92 |
- #' @examples+ #' {
|
||
| 41 | +93 |
- #' filter <- teal_slices(+ #' iris <- iris[, 1:n_cols] |
||
| 42 | +94 |
- #' teal_slice(dataname = "iris", varname = "Species", id = "species"),+ #' }, |
||
| 43 | +95 |
- #' teal_slice(dataname = "iris", varname = "Sepal.Length", id = "sepal_length"),+ #' n_cols = input$n_cols |
||
| 44 | +96 |
- #' teal_slice(+ #' ) |
||
| 45 | +97 |
- #' dataname = "iris", id = "long_petals", title = "Long petals", expr = "Petal.Length > 5"+ #' }) |
||
| 46 | +98 |
- #' ),+ #' }) |
||
| 47 | +99 |
- #' teal_slice(dataname = "mtcars", varname = "mpg", id = "mtcars_mpg"),+ #' } |
||
| 48 | +100 |
- #' mapping = list(+ #' ) |
||
| 49 | +101 |
- #' module1 = c("species", "sepal_length"),
+ #' ) |
||
| 50 | +102 |
- #' module2 = c("mtcars_mpg"),
+ #' |
||
| 51 | +103 |
- #' global_filters = "long_petals"+ #' output_decorator <- teal_transform_module( |
||
| 52 | +104 |
- #' )+ #' server = make_teal_transform_server( |
||
| 53 | +105 |
- #' )+ #' expression( |
||
| 54 | +106 |
- #'+ #' object <- rev(object) |
||
| 55 | +107 |
- #' app <- init(+ #' ) |
||
| 56 | +108 |
- #' data = teal_data(iris = iris, mtcars = mtcars),+ #' ) |
||
| 57 | +109 |
- #' modules = list(+ #' ) |
||
| 58 | +110 |
- #' module("module1"),
+ #' |
||
| 59 | +111 |
- #' module("module2")
+ #' app <- init( |
||
| 60 | +112 |
- #' ),+ #' data = teal_data(iris = iris), |
||
| 61 | +113 |
- #' filter = filter+ #' modules = example_module( |
||
| 62 | +114 |
- #' )+ #' transformators = data_transformators, |
||
| 63 | +115 |
- #'+ #' decorators = list(output_decorator) |
||
| 64 | +116 |
- #' if (interactive()) {
+ #' ) |
||
| 65 | +117 |
- #' shinyApp(app$ui, app$server)+ #' ) |
||
| 66 | +118 |
- #' }+ #' if (interactive()) {
|
||
| 67 | +119 |
- #'+ #' shinyApp(app$ui, app$server) |
||
| 68 | +120 |
- #' @export+ #' } |
||
| 69 | +121 |
- teal_slices <- function(...,+ #' |
||
| 70 | +122 |
- exclude_varnames = NULL,+ #' @name teal_transform_module |
||
| 71 | +123 |
- include_varnames = NULL,+ #' |
||
| 72 | +124 |
- count_type = NULL,+ #' @export |
||
| 73 | +125 |
- allow_add = TRUE,+ teal_transform_module <- function(ui = NULL, |
||
| 74 | +126 |
- module_specific = FALSE,+ server = function(id, data) data, |
||
| 75 | +127 |
- mapping,+ label = "transform module", |
||
| 76 | +128 |
- app_id = NULL) {
+ datanames = "all") {
|
||
| 77 | -170x | +129 | +25x |
- shiny::isolate({
+ structure( |
| 78 | -170x | +130 | +25x |
- checkmate::assert_flag(allow_add)+ list( |
| 79 | -170x | +131 | +25x |
- checkmate::assert_flag(module_specific)+ ui = ui, |
| 80 | -53x | +132 | +25x |
- if (!missing(mapping)) checkmate::assert_list(mapping, types = c("character", "NULL"), names = "named")
+ server = function(id, data) {
|
| 81 | -167x | +133 | +26x |
- checkmate::assert_string(app_id, null.ok = TRUE)+ data_out <- server(id, data) |
| 82 | +134 | |||
| 83 | -167x | -
- slices <- list(...)- |
- ||
| 84 | -167x | +135 | +26x |
- all_slice_id <- vapply(slices, `[[`, character(1L), "id")+ if (inherits(data_out, "reactive.event")) {
|
| 85 | +136 |
-
+ # This warning message partially detects when `eventReactive` is used in `data_module`. |
||
| 86 | -167x | +137 | +1x |
- if (missing(mapping)) {
+ warning( |
| 87 | -117x | +138 | +1x |
- mapping <- if (length(all_slice_id)) {
+ "teal_transform_module() ", |
| 88 | -26x | +139 | +1x |
- list(global_filters = all_slice_id)+ "Using eventReactive in teal_transform module server code should be avoided as it ", |
| 89 | -+ | |||
| 140 | +1x |
- } else {
+ "may lead to unexpected behavior. See the vignettes for more information ", |
||
| 90 | -91x | +141 | +1x |
- list()+ "(`vignette(\"data-transform-as-shiny-module\", package = \"teal\")`).", |
| 91 | -+ | |||
| 142 | +1x |
- }+ call. = FALSE |
||
| 92 | +143 |
- }+ ) |
||
| 93 | +144 | - - | -||
| 94 | -167x | -
- if (!module_specific) {
- |
- ||
| 95 | -148x | -
- mapping[setdiff(names(mapping), "global_filters")] <- NULL+ } |
||
| 96 | +145 |
- }+ |
||
| 97 | +146 | |||
| 98 | -167x | -
- failed_slice_id <- setdiff(unlist(mapping), all_slice_id)- |
- ||
| 99 | -167x | -
- if (length(failed_slice_id)) {
- |
- ||
| 100 | -1x | +147 | +26x |
- stop(sprintf(+ decorate_err_msg( |
| 101 | -1x | +148 | +26x |
- "Filters in mapping don't match any available filter.\n %s not in %s",+ assert_reactive(data_out), |
| 102 | -1x | +149 | +26x |
- toString(failed_slice_id),+ pre = sprintf("From: 'teal_transform_module()':\nA 'teal_transform_module' with \"%s\" label:", label),
|
| 103 | -1x | +150 | +26x |
- toString(all_slice_id)+ post = "Please make sure that this module returns a 'reactive` object containing 'teal_data' class of object." # nolint: line_length_linter. |
| 104 | +151 |
- ))+ ) |
||
| 105 | +152 |
- }+ } |
||
| 106 | +153 |
-
+ ), |
||
| 107 | -166x | +154 | +25x |
- tss <- teal.slice::teal_slices(+ label = label, |
| 108 | -+ | |||
| 155 | +25x |
- ...,+ datanames = datanames, |
||
| 109 | -166x | +156 | +25x |
- exclude_varnames = exclude_varnames,+ class = c("teal_transform_module", "teal_data_module")
|
| 110 | -166x | +|||
| 157 | ++ |
+ )+ |
+ ||
| 158 | +
- include_varnames = include_varnames,+ } |
|||
| 111 | -166x | +|||
| 159 | +
- count_type = count_type,+ |
|||
| 112 | -166x | +|||
| 160 | +
- allow_add = allow_add+ #' Make teal_transform_module's server |
|||
| 113 | +161 |
- )+ #' |
||
| 114 | -166x | +|||
| 162 | +
- attr(tss, "mapping") <- mapping+ #' A factory function to simplify creation of a [`teal_transform_module`]'s server. Specified `expr` |
|||
| 115 | -166x | +|||
| 163 | +
- attr(tss, "module_specific") <- module_specific+ #' is wrapped in a shiny module function and output can be passed to the `server` argument in |
|||
| 116 | -166x | +|||
| 164 | +
- attr(tss, "app_id") <- app_id+ #' [teal_transform_module()] call. Such a server function can be linked with ui and values from the |
|||
| 117 | -166x | +|||
| 165 | +
- class(tss) <- c("modules_teal_slices", class(tss))
+ #' inputs can be used in the expression. Object names specified in the expression will be substituted |
|||
| 118 | -166x | +|||
| 166 | +
- tss+ #' with the value of the respective input (matched by the name) - for example in |
|||
| 119 | +167 |
- })+ #' `expression(graph <- graph + ggtitle(title))` object `title` will be replaced with the value of |
||
| 120 | +168 |
- }+ #' `input$title`. |
||
| 121 | +169 |
-
+ #' @param expr (`language`) |
||
| 122 | +170 |
-
+ #' An R call which will be evaluated within [`teal.data::teal_data`] environment. |
||
| 123 | +171 |
- #' @rdname teal_slices+ #' @return `function(id, data)` returning `shiny` module |
||
| 124 | +172 |
- #' @export+ #' @examples |
||
| 125 | +173 |
- #' @keywords internal+ #' |
||
| 126 | +174 |
- #'+ #' trim_iris <- teal_transform_module( |
||
| 127 | +175 |
- as.teal_slices <- function(x) { # nolint: object_name.
+ #' label = "Simplified interactive transformator for iris", |
||
| 128 | -15x | +|||
| 176 | +
- checkmate::assert_list(x)+ #' datanames = "iris", |
|||
| 129 | -15x | +|||
| 177 | +
- lapply(x, checkmate::assert_list, names = "named", .var.name = "list element")+ #' ui = function(id) {
|
|||
| 130 | +178 |
-
+ #' ns <- NS(id) |
||
| 131 | -15x | +|||
| 179 | +
- attrs <- attributes(unclass(x))+ #' numericInput(ns("n_rows"), "Subset n rows", value = 6, min = 1, max = 150, step = 1)
|
|||
| 132 | -15x | +|||
| 180 | +
- ans <- lapply(x, function(x) if (is.teal_slice(x)) x else as.teal_slice(x))+ #' }, |
|||
| 133 | -15x | +|||
| 181 | +
- do.call(teal_slices, c(ans, attrs))+ #' server = make_teal_transform_server(expression(iris <- head(iris, n_rows))) |
|||
| 134 | +182 |
- }+ #' ) |
||
| 135 | +183 |
-
+ #' |
||
| 136 | +184 |
-
+ #' app <- init( |
||
| 137 | +185 |
- #' @rdname teal_slices+ #' data = teal_data(iris = iris), |
||
| 138 | +186 |
- #' @export+ #' modules = example_module(transformators = trim_iris) |
||
| 139 | +187 |
- #' @keywords internal+ #' ) |
||
| 140 | +188 |
- #'+ #' if (interactive()) {
|
||
| 141 | +189 |
- c.teal_slices <- function(...) {
+ #' shinyApp(app$ui, app$server) |
||
| 142 | -6x | +|||
| 190 | +
- x <- list(...)+ #' } |
|||
| 143 | -6x | +|||
| 191 | +
- checkmate::assert_true(all(vapply(x, is.teal_slices, logical(1L))), .var.name = "all arguments are teal_slices")+ #' |
|||
| 144 | +192 |
-
+ #' @export |
||
| 145 | -6x | +|||
| 193 | +
- all_attributes <- lapply(x, attributes)+ make_teal_transform_server <- function(expr) {
|
|||
| 146 | -6x | +194 | +3x |
- all_attributes <- coalesce_r(all_attributes)+ if (is.call(expr)) {
|
| 147 | -6x | +195 | +1x |
- all_attributes <- all_attributes[names(all_attributes) != "class"]+ expr <- as.expression(expr) |
| 148 | +196 |
-
+ } |
||
| 149 | -6x | +197 | +3x |
- do.call(+ checkmate::assert_multi_class(expr, c("call", "expression"))
+ |
+
| 198 | ++ | + | ||
| 150 | -6x | +199 | +3x |
- teal_slices,+ function(id, data) {
|
| 151 | -6x | +200 | +3x |
- c(+ moduleServer(id, function(input, output, session) {
|
| 152 | -6x | +201 | +3x |
- unique(unlist(x, recursive = FALSE)),+ list_env <- reactive( |
| 153 | -6x | +202 | +3x |
- all_attributes+ lapply(rlang::set_names(names(input)), function(x) input[[x]]) |
| 154 | +203 |
- )+ ) |
||
| 155 | +204 |
- )+ |
||
| 156 | -+ | |||
| 205 | +3x |
- }+ reactive({
|
||
| 157 | -+ | |||
| 206 | +4x |
-
+ call_with_inputs <- lapply(expr, function(x) {
|
||
| 158 | -+ | |||
| 207 | +4x |
-
+ do.call(what = substitute, args = list(expr = x, env = list_env())) |
||
| 159 | +208 |
- #' Deep copy `teal_slices`+ }) |
||
| 160 | -+ | |||
| 209 | +4x |
- #'+ eval_code(object = data(), code = as.expression(call_with_inputs)) |
||
| 161 | +210 |
- #' it's important to create a new copy of `teal_slices` when+ }) |
||
| 162 | +211 |
- #' starting a new `shiny` session. Otherwise, object will be shared+ }) |
||
| 163 | +212 |
- #' by multiple users as it is created in global environment before+ } |
||
| 164 | +213 |
- #' `shiny` session starts.+ } |
||
| 165 | +214 |
- #' @param filter (`teal_slices`)+ |
||
| 166 | +215 |
- #' @return `teal_slices`+ #' Extract all `transformators` from `modules`. |
||
| 167 | +216 |
- #' @keywords internal+ #' |
||
| 168 | +217 |
- deep_copy_filter <- function(filter) {
+ #' @param modules `teal_modules` or `teal_module` |
||
| 169 | -1x | +|||
| 218 | +
- checkmate::assert_class(filter, "teal_slices")+ #' @return A list of `teal_transform_module` nested in the same way as input `modules`. |
|||
| 170 | -1x | +|||
| 219 | +
- shiny::isolate({
+ #' @keywords internal |
|||
| 171 | -1x | +|||
| 220 | +
- filter_copy <- lapply(filter, function(slice) {
+ extract_transformators <- function(modules) {
|
|||
| 172 | -2x | +221 | +10x |
- teal.slice::as.teal_slice(as.list(slice))+ if (inherits(modules, "teal_module")) {
|
| 173 | -+ | |||
| 222 | +5x |
- })+ modules$transformators |
||
| 174 | -1x | +223 | +5x |
- attributes(filter_copy) <- attributes(filter)+ } else if (inherits(modules, "teal_modules")) {
|
| 175 | -1x | +224 | +5x |
- filter_copy+ lapply(modules$children, extract_transformators) |
| 176 | +225 |
- })+ } |
||
| 177 | +226 |
}@@ -16958,7010 +16197,6966 @@ teal coverage - 60.11% |
| 1 |
- # This is the main function from teal to be used by the end-users. Although it delegates+ #' An example `teal` module |
|||
| 2 |
- # directly to `module_teal_with_splash.R`, we keep it in a separate file because its documentation is quite large+ #' |
|||
| 3 |
- # and it is very end-user oriented. It may also perform more argument checking with more informative+ #' `r lifecycle::badge("experimental")`
|
|||
| 4 |
- # error messages.+ #' |
|||
| 5 |
-
+ #' This module creates an object called `object` that can be modified with decorators. |
|||
| 6 |
- #' Create the server and UI function for the `shiny` app+ #' The `object` is determined by what's selected in `Choose a dataset` input in UI. |
|||
| 7 |
- #'+ #' The object can be anything that can be handled by `renderPrint()`. |
|||
| 8 |
- #' @description `r lifecycle::badge("stable")`
+ #' See the `vignette("decorate-modules-output", package = "teal")` or [`teal_transform_module`]
|
|||
| 9 |
- #'+ #' to read more about decorators. |
|||
| 10 |
- #' End-users: This is the most important function for you to start a+ #' |
|||
| 11 |
- #' `teal` app that is composed of `teal` modules.+ #' @inheritParams teal_modules |
|||
| 12 |
- #'+ #' @param decorators `r lifecycle::badge("experimental")` (`list` of `teal_transform_module` or `NULL`) optional,
|
|||
| 13 |
- #' @param data (`teal_data` or `teal_data_module`)+ #' if not `NULL`, decorator for tables or plots included in the module. |
|||
| 14 |
- #' For constructing the data object, refer to [teal.data::teal_data()] and [teal_data_module()].+ #' |
|||
| 15 |
- #' If `datanames` are not set for the `teal_data` object, defaults from the `teal_data` environment will be used.+ #' @return A `teal` module which can be included in the `modules` argument to [init()]. |
|||
| 16 |
- #' @param modules (`list` or `teal_modules` or `teal_module`)+ #' @examples |
|||
| 17 |
- #' Nested list of `teal_modules` or `teal_module` objects or a single+ #' app <- init( |
|||
| 18 |
- #' `teal_modules` or `teal_module` object. These are the specific output modules which+ #' data = teal_data(IRIS = iris, MTCARS = mtcars), |
|||
| 19 |
- #' will be displayed in the `teal` application. See [modules()] and [module()] for+ #' modules = example_module() |
|||
| 20 |
- #' more details.+ #' ) |
|||
| 21 |
- #' @param filter (`teal_slices`) Optionally,+ #' if (interactive()) {
|
|||
| 22 |
- #' specifies the initial filter using [teal_slices()].+ #' shinyApp(app$ui, app$server) |
|||
| 23 |
- #' @param title (`shiny.tag` or `character(1)`) Optionally,+ #' } |
|||
| 24 |
- #' the browser window title. Defaults to a title "teal app" with the icon of NEST.+ #' @export |
|||
| 25 |
- #' Can be created using the `build_app_title()` or+ example_module <- function(label = "example teal module", |
|||
| 26 |
- #' by passing a valid `shiny.tag` which is a head tag with title and link tag.+ datanames = "all", |
|||
| 27 |
- #' @param header (`shiny.tag` or `character(1)`) Optionally,+ transformators = list(), |
|||
| 28 |
- #' the header of the app.+ decorators = NULL) {
|
|||
| 29 | -+ | 43x |
- #' @param footer (`shiny.tag` or `character(1)`) Optionally,+ checkmate::assert_string(label) |
|
| 30 | -+ | 43x |
- #' the footer of the app.+ checkmate::assert_list(decorators, "teal_transform_module", null.ok = TRUE) |
|
| 31 |
- #' @param id (`character`) Optionally,+ |
|||
| 32 | -+ | 43x |
- #' a string specifying the `shiny` module id in cases it is used as a `shiny` module+ ans <- module( |
|
| 33 | -+ | 43x |
- #' rather than a standalone `shiny` app. This is a legacy feature.+ label, |
|
| 34 | -+ | 43x |
- #' @param landing_popup (`teal_module_landing`) Optionally,+ server = function(id, data, decorators) {
|
|
| 35 | -+ | 5x |
- #' a `landing_popup_module` to show up as soon as the teal app is initialized.+ checkmate::assert_class(isolate(data()), "teal_data") |
|
| 36 | -+ | 5x |
- #'+ moduleServer(id, function(input, output, session) {
|
|
| 37 | -+ | 5x |
- #' @return Named list containing server and UI functions.+ datanames_rv <- reactive(names(req(data()))) |
|
| 38 | -+ | 5x |
- #'+ observeEvent(datanames_rv(), {
|
|
| 39 | -+ | 5x |
- #' @export+ selected <- input$dataname |
|
| 40 | -+ | 5x |
- #'+ if (identical(selected, "")) {
|
|
| 41 | -+ | ! |
- #' @include modules.R+ selected <- restoreInput(session$ns("dataname"), NULL)
|
|
| 42 | -+ | 5x |
- #'+ } else if (isFALSE(selected %in% datanames_rv())) {
|
|
| 43 | -+ | ! |
- #' @examples+ selected <- datanames_rv()[1] |
|
| 44 |
- #' app <- init(+ } |
|||
| 45 | -+ | 5x |
- #' data = within(+ updateSelectInput( |
|
| 46 | -+ | 5x |
- #' teal_data(),+ session = session, |
|
| 47 | -+ | 5x |
- #' {
+ inputId = "dataname", |
|
| 48 | -+ | 5x |
- #' new_iris <- transform(iris, id = seq_len(nrow(iris)))+ choices = datanames_rv(), |
|
| 49 | -+ | 5x |
- #' new_mtcars <- transform(mtcars, id = seq_len(nrow(mtcars)))+ selected = selected |
|
| 50 |
- #' }+ ) |
|||
| 51 |
- #' ),+ }) |
|||
| 52 |
- #' modules = modules(+ |
|||
| 53 | -+ | 5x |
- #' module(+ table_data <- reactive({
|
|
| 54 | -+ | 8x |
- #' label = "data source",+ req(input$dataname) |
|
| 55 | -+ | 3x |
- #' server = function(input, output, session, data) {},
+ within(data(), |
|
| 56 |
- #' ui = function(id, ...) tags$div(p("information about data source")),
+ {
|
|||
| 57 | -+ | 3x |
- #' datanames = "all"+ object <- dataname |
|
| 58 |
- #' ),+ }, |
|||
| 59 | -+ | 3x |
- #' example_module(label = "example teal module"),+ dataname = as.name(input$dataname) |
|
| 60 |
- #' module(+ ) |
|||
| 61 |
- #' "Iris Sepal.Length histogram",+ }) |
|||
| 62 |
- #' server = function(input, output, session, data) {
+
|
|||
| 63 | -+ | 5x |
- #' output$hist <- renderPlot(+ table_data_decorated_no_print <- srv_transform_teal_data( |
|
| 64 | -+ | 5x |
- #' hist(data()[["new_iris"]]$Sepal.Length)+ "decorate", |
|
| 65 | -+ | 5x |
- #' )+ data = table_data, |
|
| 66 | -+ | 5x |
- #' },+ transformators = decorators |
|
| 67 |
- #' ui = function(id, ...) {
+ ) |
|||
| 68 | -+ | 5x |
- #' ns <- NS(id)+ table_data_decorated <- reactive(within(req(table_data_decorated_no_print()), expr = object)) |
|
| 69 |
- #' plotOutput(ns("hist"))
+
|
|||
| 70 | -+ | 5x |
- #' },+ output$text <- renderPrint({
|
|
| 71 | -+ | 9x |
- #' datanames = "new_iris"+ req(table_data()) # Ensure original errors from module are displayed |
|
| 72 | -+ | 4x |
- #' )+ table_data_decorated()[["object"]] |
|
| 73 |
- #' ),+ }) |
|||
| 74 |
- #' filter = teal_slices(+ |
|||
| 75 | -+ | 5x |
- #' teal_slice(dataname = "new_iris", varname = "Species"),+ teal.widgets::verbatim_popup_srv( |
|
| 76 | -+ | 5x |
- #' teal_slice(dataname = "new_iris", varname = "Sepal.Length"),+ id = "rcode", |
|
| 77 | -+ | 5x |
- #' teal_slice(dataname = "new_mtcars", varname = "cyl"),+ verbatim_content = reactive(teal.code::get_code(req(table_data_decorated()))), |
|
| 78 | -+ | 5x |
- #' exclude_varnames = list(new_iris = c("Sepal.Width", "Petal.Width")),
+ title = "Example Code" |
|
| 79 |
- #' module_specific = TRUE,+ ) |
|||
| 80 |
- #' mapping = list(+ |
|||
| 81 | -+ | 5x |
- #' `example teal module` = "new_iris Species",+ table_data_decorated |
|
| 82 |
- #' `Iris Sepal.Length histogram` = "new_iris Species",+ }) |
|||
| 83 |
- #' global_filters = "new_mtcars cyl"+ }, |
|||
| 84 | -+ | 43x |
- #' )+ ui = function(id, decorators) {
|
|
| 85 | -+ | ! |
- #' ),+ ns <- NS(id) |
|
| 86 | -+ | ! |
- #' title = "App title",+ teal.widgets::standard_layout( |
|
| 87 | -+ | ! |
- #' header = tags$h1("Sample App"),
+ output = verbatimTextOutput(ns("text")),
|
|
| 88 | -+ | ! |
- #' footer = tags$p("Sample footer")
+ encoding = tags$div( |
|
| 89 | -+ | ! |
- #' )+ selectInput(ns("dataname"), "Choose a dataset", choices = NULL),
|
|
| 90 | -+ | ! |
- #' if (interactive()) {
+ ui_transform_teal_data(ns("decorate"), transformators = decorators),
|
|
| 91 | -+ | ! |
- #' shinyApp(app$ui, app$server)+ teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
|
|
| 92 |
- #' }+ ) |
|||
| 93 |
- #'+ ) |
|||
| 94 |
- init <- function(data,+ }, |
|||
| 95 | -+ | 43x |
- modules,+ ui_args = list(decorators = decorators), |
|
| 96 | -+ | 43x |
- filter = teal_slices(),+ server_args = list(decorators = decorators), |
|
| 97 | -+ | 43x |
- title = build_app_title(),+ datanames = datanames, |
|
| 98 | -+ | 43x |
- header = tags$p(),+ transformators = transformators |
|
| 99 |
- footer = tags$p(),+ ) |
|||
| 100 | -- |
- id = character(0),- |
- ||
| 101 | -+ | 43x |
- landing_popup = NULL) {
+ attr(ans, "teal_bookmarkable") <- TRUE |
|
| 102 | -14x | +101 | +43x |
- logger::log_debug("init initializing teal app with: data ('{ class(data) }').")
+ ans |
| 103 | +102 |
-
+ } |
| 104 | +1 |
- # argument checking (independent)+ #' Get client timezone |
||
| 105 | +2 |
- ## `data`- |
- ||
| 106 | -14x | -
- checkmate::assert_multi_class(data, c("teal_data", "teal_data_module"))
- |
- ||
| 107 | -14x | -
- checkmate::assert_class(landing_popup, "teal_module_landing", null.ok = TRUE)+ #' |
||
| 108 | +3 |
-
+ #' User timezone in the browser may be different to the one on the server. |
||
| 109 | +4 |
- ## `modules`- |
- ||
| 110 | -14x | -
- checkmate::assert(- |
- ||
| 111 | -14x | -
- .var.name = "modules",- |
- ||
| 112 | -14x | -
- checkmate::check_multi_class(modules, c("teal_modules", "teal_module")),
- |
- ||
| 113 | -14x | -
- checkmate::check_list(modules, min.len = 1, any.missing = FALSE, types = c("teal_module", "teal_modules"))
+ #' This script can be run to register a `shiny` input which contains information about the timezone in the browser. |
||
| 114 | +5 |
- )- |
- ||
| 115 | -14x | -
- if (inherits(modules, "teal_module")) {
- |
- ||
| 116 | -1x | -
- modules <- list(modules)+ #' |
||
| 117 | +6 |
- }- |
- ||
| 118 | -14x | -
- if (checkmate::test_list(modules, min.len = 1, any.missing = FALSE, types = c("teal_module", "teal_modules"))) {
- |
- ||
| 119 | -8x | -
- modules <- do.call(teal::modules, modules)+ #' @param ns (`function`) namespace function passed from the `session` object in the `shiny` server. |
||
| 120 | +7 |
- }+ #' For `shiny` modules this will allow for proper name spacing of the registered input. |
||
| 121 | +8 |
-
+ #' |
||
| 122 | +9 |
- ## `filter`- |
- ||
| 123 | -14x | -
- checkmate::assert_class(filter, "teal_slices")+ #' @return `NULL`, invisibly. |
||
| 124 | +10 |
-
+ #' |
||
| 125 | +11 |
- ## all other arguments- |
- ||
| 126 | -13x | -
- checkmate::assert(- |
- ||
| 127 | -13x | -
- .var.name = "title",- |
- ||
| 128 | -13x | -
- checkmate::check_string(title),- |
- ||
| 129 | -13x | -
- checkmate::check_multi_class(title, c("shiny.tag", "shiny.tag.list", "html"))
+ #' @keywords internal |
||
| 130 | +12 |
- )- |
- ||
| 131 | -13x | -
- checkmate::assert(- |
- ||
| 132 | -13x | -
- .var.name = "header",- |
- ||
| 133 | -13x | -
- checkmate::check_string(header),- |
- ||
| 134 | -13x | -
- checkmate::check_multi_class(header, c("shiny.tag", "shiny.tag.list", "html"))
+ #' |
||
| 135 | +13 |
- )- |
- ||
| 136 | -13x | -
- checkmate::assert(+ get_client_timezone <- function(ns) {
|
||
| 137 | -13x | +14 | +88x |
- .var.name = "footer",+ script <- sprintf( |
| 138 | -13x | +15 | +88x |
- checkmate::check_string(footer),+ "Shiny.setInputValue(`%s`, Intl.DateTimeFormat().resolvedOptions().timeZone)", |
| 139 | -13x | +16 | +88x |
- checkmate::check_multi_class(footer, c("shiny.tag", "shiny.tag.list", "html"))
+ ns("timezone")
|
| 140 | +17 |
) |
||
| 141 | -13x | +18 | +88x |
- checkmate::assert_character(id, max.len = 1, any.missing = FALSE)+ shinyjs::runjs(script) # function does not return anything+ |
+
| 19 | +88x | +
+ invisible(NULL) |
||
| 142 | +20 |
-
+ } |
||
| 143 | +21 |
- # log+ |
||
| 144 | -13x | +|||
| 22 | +
- teal.logger::log_system_info()+ #' Resolve the expected bootstrap theme |
|||
| 145 | +23 |
-
+ #' @noRd |
||
| 146 | +24 |
- # argument transformations+ #' @keywords internal |
||
| 147 | +25 |
- ## `modules` - landing module+ get_teal_bs_theme <- function() {
|
||
| 148 | -13x | +26 | +4x |
- landing <- extract_module(modules, "teal_module_landing")+ bs_theme <- getOption("teal.bs_theme")
|
| 149 | -13x | +|||
| 27 | +
- if (length(landing) == 1L) {
+
|
|||
| 150 | -! | +|||
| 28 | +4x |
- landing_popup <- landing[[1L]]+ if (is.null(bs_theme)) {
|
||
| 151 | -! | +|||
| 29 | +1x |
- modules <- drop_module(modules, "teal_module_landing")+ return(NULL) |
||
| 152 | -! | +|||
| 30 | +
- lifecycle::deprecate_soft(+ } |
|||
| 153 | -! | +|||
| 31 | +
- when = "0.15.3",+ |
|||
| 154 | -! | +|||
| 32 | +3x |
- what = "landing_popup_module()",+ if (!checkmate::test_class(bs_theme, "bs_theme")) {
|
||
| 155 | -! | +|||
| 33 | +2x |
- details = paste(+ warning( |
||
| 156 | -! | +|||
| 34 | +2x |
- "Pass `landing_popup_module` to the `landing_popup` argument of the `init` ",+ "Assertion on 'teal.bs_theme' option value failed: ", |
||
| 157 | -! | +|||
| 35 | +2x |
- "instead of wrapping it into `modules()` and passing to the `modules` argument"+ checkmate::check_class(bs_theme, "bs_theme"), |
||
| 158 | -+ | |||
| 36 | +2x |
- )+ ". The default Shiny Bootstrap theme will be used." |
||
| 159 | +37 |
) |
||
| 160 | -13x | -
- } else if (length(landing) > 1L) {
- |
- ||
| 161 | -! | +38 | +2x |
- stop("Only one `landing_popup_module` can be used.")
+ return(NULL) |
| 162 | +39 |
} |
||
| 163 | +40 | |||
| 164 | -- |
- ## `filter` - set app_id attribute unless present (when restoring bookmark)- |
- ||
| 165 | -13x | +41 | +1x |
- if (is.null(attr(filter, "app_id", exact = TRUE))) attr(filter, "app_id") <- create_app_id(data, modules)+ bs_theme |
| 166 | +42 |
-
+ } |
||
| 167 | +43 |
- ## `filter` - convert teal.slice::teal_slices to teal::teal_slices+ |
||
| 168 | -13x | +|||
| 44 | +
- filter <- as.teal_slices(as.list(filter))+ #' Return parentnames along with datanames. |
|||
| 169 | +45 |
-
+ #' @noRd |
||
| 170 | +46 |
- # argument checking (interdependent)+ #' @keywords internal |
||
| 171 | +47 |
- ## `filter` - `modules`+ .include_parent_datanames <- function(datanames, join_keys) {
|
||
| 172 | -13x | +48 | +32x |
- if (isTRUE(attr(filter, "module_specific"))) {
+ ordered_datanames <- datanames |
| 173 | -! | +|||
| 49 | +32x |
- module_names <- unlist(c(module_labels(modules), "global_filters"))+ for (current in datanames) {
|
||
| 174 | -! | +|||
| 50 | +62x |
- failed_mod_names <- setdiff(names(attr(filter, "mapping")), module_names)+ parents <- character(0L) |
||
| 175 | -! | +|||
| 51 | +62x |
- if (length(failed_mod_names)) {
+ while (length(current) > 0) {
|
||
| 176 | -! | +|||
| 52 | +64x |
- stop(+ current <- teal.data::parent(join_keys, current) |
||
| 177 | -! | +|||
| 53 | +64x |
- sprintf(+ parents <- c(current, parents) |
||
| 178 | -! | +|||
| 54 | +
- "Some module names in the mapping arguments don't match module labels.\n %s not in %s",+ } |
|||
| 179 | -! | +|||
| 55 | +62x |
- toString(failed_mod_names),+ ordered_datanames <- c(parents, ordered_datanames) |
||
| 180 | -! | +|||
| 56 | +
- toString(unique(module_names))+ } |
|||
| 181 | +57 |
- )+ |
||
| 182 | -+ | |||
| 58 | +32x |
- )+ unique(ordered_datanames) |
||
| 183 | +59 |
- }+ } |
||
| 184 | +60 | |||
| 185 | -! | +|||
| 61 | +
- if (anyDuplicated(module_names)) {
+ #' Create a `FilteredData` |
|||
| 186 | +62 |
- # In teal we are able to set nested modules with duplicated label.+ #' |
||
| 187 | +63 |
- # Because mapping argument bases on the relationship between module-label and filter-id,+ #' Create a `FilteredData` object from a `teal_data` object. |
||
| 188 | +64 |
- # it is possible that module-label in mapping might refer to multiple teal_module (identified by the same label)+ #' |
||
| 189 | -! | +|||
| 65 | +
- stop(+ #' @param x (`teal_data`) object |
|||
| 190 | -! | +|||
| 66 | +
- sprintf(+ #' @param datanames (`character`) vector of data set names to include; must be subset of `names(x)` |
|||
| 191 | -! | +|||
| 67 | +
- "Module labels should be unique when teal_slices(mapping = TRUE). Duplicated labels:\n%s ",+ #' @return A `FilteredData` object. |
|||
| 192 | -! | +|||
| 68 | +
- toString(module_names[duplicated(module_names)])+ #' @keywords internal |
|||
| 193 | +69 |
- )+ teal_data_to_filtered_data <- function(x, datanames = names(x)) {
|
||
| 194 | -+ | |||
| 70 | +83x |
- )+ checkmate::assert_class(x, "teal_data") |
||
| 195 | -+ | |||
| 71 | +83x |
- }+ checkmate::assert_character(datanames, min.chars = 1L, any.missing = FALSE) |
||
| 196 | +72 |
- }+ # Otherwise, FilteredData will be created in the modules' scope later+ |
+ ||
| 73 | +83x | +
+ teal.slice::init_filtered_data(+ |
+ ||
| 74 | +83x | +
+ x = Filter(length, sapply(datanames, function(dn) x[[dn]], simplify = FALSE)),+ |
+ ||
| 75 | +83x | +
+ join_keys = teal.data::join_keys(x) |
||
| 197 | +76 |
-
+ ) |
||
| 198 | +77 |
- ## `data` - `modules`+ } |
||
| 199 | -13x | +|||
| 78 | +
- if (inherits(data, "teal_data")) {
+
|
|||
| 200 | -12x | +|||
| 79 | +
- if (length(data) == 0) {
+
|
|||
| 201 | -1x | +|||
| 80 | +
- stop("The environment of `data` is empty.")
+ #' Template function for `TealReportCard` creation and customization |
|||
| 202 | +81 |
- }+ #' |
||
| 203 | +82 |
-
+ #' This function generates a report card with a title, |
||
| 204 | -11x | +|||
| 83 | +
- is_modules_ok <- check_modules_datanames(modules, names(data))+ #' an optional description, and the option to append the filter state list. |
|||
| 205 | -11x | +|||
| 84 | +
- if (!isTRUE(is_modules_ok) && length(unlist(extract_transformators(modules))) == 0) {
+ #' |
|||
| 206 | -4x | +|||
| 85 | +
- warning(is_modules_ok, call. = FALSE)+ #' @param title (`character(1)`) title of the card (unless overwritten by label) |
|||
| 207 | +86 |
- }+ #' @param label (`character(1)`) label provided by the user when adding the card |
||
| 208 | +87 |
-
+ #' @param description (`character(1)`) optional, additional description |
||
| 209 | -11x | +|||
| 88 | +
- is_filter_ok <- check_filter_datanames(filter, names(data))+ #' @param with_filter (`logical(1)`) flag indicating to add filter state |
|||
| 210 | -11x | +|||
| 89 | +
- if (!isTRUE(is_filter_ok)) {
+ #' @param filter_panel_api (`FilterPanelAPI`) object with API that allows the generation |
|||
| 211 | -1x | +|||
| 90 | +
- warning(is_filter_ok)+ #' of the filter state in the report |
|||
| 212 | +91 |
- # we allow app to continue if applied filters are outside+ #' |
||
| 213 | +92 |
- # of possible data range+ #' @return (`TealReportCard`) populated with a title, description and filter state. |
||
| 214 | +93 |
- }+ #' |
||
| 215 | +94 |
- }+ #' @export |
||
| 216 | +95 |
-
+ report_card_template <- function(title, label, description = NULL, with_filter, filter_panel_api) {
|
||
| 217 | -12x | +96 | +2x |
- reporter <- teal.reporter::Reporter$new()$set_id(attr(filter, "app_id"))+ checkmate::assert_string(title) |
| 218 | -12x | +97 | +2x |
- if (is_arg_used(modules, "reporter") && length(extract_module(modules, "teal_module_previewer")) == 0) {
+ checkmate::assert_string(label) |
| 219 | -! | +|||
| 98 | +2x |
- modules <- append_module(+ checkmate::assert_string(description, null.ok = TRUE) |
||
| 220 | -! | +|||
| 99 | +2x |
- modules,+ checkmate::assert_flag(with_filter) |
||
| 221 | -! | +|||
| 100 | +2x |
- reporter_previewer_module(server_args = list(previewer_buttons = c("download", "reset")))
+ checkmate::assert_class(filter_panel_api, classes = "FilterPanelAPI") |
||
| 222 | +101 |
- )+ |
||
| 223 | -+ | |||
| 102 | +2x |
- }+ card <- teal::TealReportCard$new() |
||
| 224 | -+ | |||
| 103 | +2x |
-
+ title <- if (label == "") title else label |
||
| 225 | -12x | +104 | +2x |
- ns <- NS(id)+ card$set_name(title) |
| 226 | -+ | |||
| 105 | +2x |
- # Note: UI must be a function to support bookmarking.+ card$append_text(title, "header2") |
||
| 227 | -12x | +106 | +1x |
- res <- list(+ if (!is.null(description)) card$append_text(description, "header3") |
| 228 | -12x | +107 | +1x |
- ui = function(request) {
+ if (with_filter) card$append_fs(filter_panel_api$get_filter_state()) |
| 229 | -! | +|||
| 108 | +2x |
- ui_teal(+ card |
||
| 230 | -! | +|||
| 109 | +
- id = ns("teal"),
+ } |
|||
| 231 | -! | +|||
| 110 | +
- modules = modules,+ |
|||
| 232 | -! | +|||
| 111 | +
- title = title,+ |
|||
| 233 | -! | +|||
| 112 | +
- header = header,+ #' Check `datanames` in modules |
|||
| 234 | -! | +|||
| 113 | +
- footer = footer+ #' |
|||
| 235 | +114 |
- )+ #' These functions check if specified `datanames` in modules match those in the data object, |
||
| 236 | +115 |
- },+ #' returning error messages or `TRUE` for successful validation. Two functions return error message |
||
| 237 | -12x | +|||
| 116 | +
- server = function(input, output, session) {
+ #' in different forms: |
|||
| 238 | -! | +|||
| 117 | +
- if (!is.null(landing_popup)) {
+ #' - `check_modules_datanames` returns `character(1)` for basic assertion usage |
|||
| 239 | -! | +|||
| 118 | +
- do.call(landing_popup$server, c(list(id = "landing_module_shiny_id"), landing_popup$server_args))+ #' - `check_modules_datanames_html` returns `shiny.tag.list` to display it in the app. |
|||
| 240 | +119 |
- }+ #' |
||
| 241 | -! | +|||
| 120 | +
- srv_teal(id = ns("teal"), data = data, modules = modules, filter = deep_copy_filter(filter))
+ #' @param modules (`teal_modules`) object |
|||
| 242 | +121 |
- }+ #' @param datanames (`character`) names of datasets available in the `data` object |
||
| 243 | +122 |
- )+ #' |
||
| 244 | +123 |
-
+ #' @return `TRUE` if validation passes, otherwise `character(1)` or `shiny.tag.list` |
||
| 245 | -12x | +|||
| 124 | +
- logger::log_debug("init teal app has been initialized.")
+ #' @keywords internal |
|||
| 246 | +125 |
-
+ check_modules_datanames <- function(modules, datanames) {
|
||
| 247 | -12x | +126 | +11x |
- res+ out <- check_modules_datanames_html(modules, datanames) |
| 248 | -+ | |||
| 127 | +11x |
- }+ if (inherits(out, "shiny.tag.list")) {
|
| 1 | -+ | |||
| 128 | +5x |
- setOldClass("teal_module")
+ out_with_ticks <- gsub("<code>|</code>", "`", toString(out))
|
||
| 2 | -+ | |||
| 129 | +5x |
- setOldClass("teal_modules")
+ out_text <- gsub("<[^<>]+>", "", toString(out_with_ticks))
|
||
| 3 | -+ | |||
| 130 | +5x |
-
+ trimws(gsub("[[:space:]]+", " ", out_text))
|
||
| 4 | +131 |
- #' Create `teal_module` and `teal_modules` objects+ } else {
|
||
| 5 | -+ | |||
| 132 | +6x |
- #'+ out |
||
| 6 | +133 |
- #' @description+ } |
||
| 7 | +134 |
- #' `r lifecycle::badge("stable")`
+ } |
||
| 8 | +135 |
- #' Create a nested tab structure to embed modules in a `teal` application.+ |
||
| 9 | +136 |
- #'+ #' @rdname check_modules_datanames |
||
| 10 | +137 |
- #' @details+ check_reserved_datanames <- function(datanames) {
|
||
| 11 | -+ | |||
| 138 | +190x |
- #' `module()` creates an instance of a `teal_module` that can be placed in a `teal` application.+ reserved_datanames <- datanames[datanames %in% c("all", ".raw_data")]
|
||
| 12 | -+ | |||
| 139 | +190x |
- #' `modules()` shapes the structure of a the application by organizing `teal_module` within the navigation panel.+ if (length(reserved_datanames) == 0L) {
|
||
| 13 | -+ | |||
| 140 | +184x |
- #' It wraps `teal_module` and `teal_modules` objects in a `teal_modules` object,+ return(NULL) |
||
| 14 | +141 |
- #' which results in a nested structure corresponding to the nested tabs in the final application.+ } |
||
| 15 | +142 |
- #'+ |
||
| 16 | -+ | |||
| 143 | +6x |
- #' Note that for `modules()` `label` comes after `...`, so it must be passed as a named argument,+ tags$span( |
||
| 17 | -+ | |||
| 144 | +6x |
- #' otherwise it will be captured by `...`.+ to_html_code_list(reserved_datanames), |
||
| 18 | -+ | |||
| 145 | +6x |
- #'+ sprintf( |
||
| 19 | -+ | |||
| 146 | +6x |
- #' The labels `"global_filters"` and `"Report previewer"` are reserved+ "%s reserved for internal use. Please avoid using %s as %s.", |
||
| 20 | -+ | |||
| 147 | +6x |
- #' because they are used by the `mapping` argument of [teal_slices()]+ pluralize(reserved_datanames, "is", "are"), |
||
| 21 | -+ | |||
| 148 | +6x |
- #' and the report previewer module [reporter_previewer_module()], respectively.+ pluralize(reserved_datanames, "it", "them"), |
||
| 22 | -+ | |||
| 149 | +6x |
- #'+ pluralize(reserved_datanames, "a dataset name", "dataset names") |
||
| 23 | +150 |
- #' # Restricting datasets used by `teal_module`:+ ) |
||
| 24 | +151 |
- #' The `datanames` argument controls which datasets are used by the module’s server. These datasets,+ ) |
||
| 25 | +152 |
- #' passed via server's `data` argument, are the only ones shown in the module's tab.+ } |
||
| 26 | +153 |
- #'+ |
||
| 27 | +154 |
- #' When `datanames` is set to `"all"`, all datasets in the data object are treated as relevant.+ #' @rdname check_modules_datanames |
||
| 28 | +155 |
- #' However, this may include unnecessary datasets, such as:+ check_modules_datanames_html <- function(modules, datanames) {
|
||
| 29 | -+ | |||
| 156 | +190x |
- #' - Proxy variables for column modifications+ check_datanames <- check_modules_datanames_recursive(modules, datanames) |
||
| 30 | -+ | |||
| 157 | +190x |
- #' - Temporary datasets used to create final versions+ show_module_info <- inherits(modules, "teal_modules") # used in two contexts - module and app |
||
| 31 | +158 |
- #' - Connection objects+ |
||
| 32 | -+ | |||
| 159 | +190x |
- #'+ reserved_datanames <- check_reserved_datanames(datanames) |
||
| 33 | +160 |
- #' To exclude irrelevant datasets, use the [set_datanames()] function to change `datanames` from+ |
||
| 34 | -+ | |||
| 161 | +190x |
- #' `"all"` to specific names. Trying to modify non-`"all"` values with [set_datanames()] will result+ if (!length(check_datanames)) {
|
||
| 35 | -+ | |||
| 162 | +172x |
- #' in a warning. Datasets with names starting with . are ignored globally unless explicitly listed+ out <- if (is.null(reserved_datanames)) {
|
||
| 36 | -+ | |||
| 163 | +166x |
- #' in `datanames`.+ TRUE |
||
| 37 | +164 |
- #'+ } else {
|
||
| 38 | -+ | |||
| 165 | +6x |
- #' # `datanames` with `transformators`+ shiny::tagList(reserved_datanames) |
||
| 39 | +166 |
- #' When transformators are specified, their `datanames` are added to the module’s `datanames`, which+ } |
||
| 40 | -+ | |||
| 167 | +172x |
- #' changes the behavior as follows:+ return(out) |
||
| 41 | +168 |
- #' - If `module(datanames)` is `NULL` and the `transformators` have defined `datanames`, the sidebar+ } |
||
| 42 | -+ | |||
| 169 | +18x |
- #' will appear showing the `transformators`' datasets, instead of being hidden.+ shiny::tagList( |
||
| 43 | -+ | |||
| 170 | +18x |
- #' - If `module(datanames)` is set to specific values and any `transformator` has `datanames = "all"`,+ reserved_datanames, |
||
| 44 | -+ | |||
| 171 | +18x |
- #' the module may receive extra datasets that could be unnecessary+ lapply( |
||
| 45 | -+ | |||
| 172 | +18x |
- #'+ check_datanames, |
||
| 46 | -+ | |||
| 173 | +18x |
- #' @param label (`character(1)`) Label shown in the navigation item for the module or module group.+ function(mod) {
|
||
| 47 | -+ | |||
| 174 | +18x |
- #' For `modules()` defaults to `"root"`. See `Details`.+ tagList( |
||
| 48 | -+ | |||
| 175 | +18x | +
+ tags$span(+ |
+ ||
| 176 | +18x | +
+ tags$span(pluralize(mod$missing_datanames, "Dataset")),+ |
+ ||
| 177 | +18x |
- #' @param server (`function`) `shiny` module with following arguments:+ to_html_code_list(mod$missing_datanames), |
||
| 49 | -+ | |||
| 178 | +18x |
- #' - `id` - `teal` will set proper `shiny` namespace for this module (see [shiny::moduleServer()]).+ tags$span( |
||
| 50 | -+ | |||
| 179 | +18x |
- #' - `input`, `output`, `session` - (optional; not recommended) When provided, then [shiny::callModule()]+ sprintf( |
||
| 51 | -+ | |||
| 180 | +18x |
- #' will be used to call a module. From `shiny` 1.5.0, the recommended way is to use+ "%s missing%s.", |
||
| 52 | -+ | |||
| 181 | +18x |
- #' [shiny::moduleServer()] instead which doesn't require these arguments.+ pluralize(mod$missing_datanames, "is", "are"), |
||
| 53 | -+ | |||
| 182 | +18x |
- #' - `data` (optional) When provided, the module will be called with `teal_data` object (i.e. a list of+ if (show_module_info) sprintf(" for module '%s'", mod$label) else ""
|
||
| 54 | +183 |
- #' reactive (filtered) data specified in the `filters` argument) as the value of this argument.+ ) |
||
| 55 | +184 |
- #' - `datasets` (optional) When provided, the module will be called with `FilteredData` object as the+ ) |
||
| 56 | +185 |
- #' value of this argument. (See [`teal.slice::FilteredData`]).+ ), |
||
| 57 | -+ | |||
| 186 | +18x |
- #' - `reporter` (optional) When provided, the module will be called with `Reporter` object as the value+ if (length(datanames) >= 1) {
|
||
| 58 | -+ | |||
| 187 | +16x |
- #' of this argument. (See [`teal.reporter::Reporter`]).+ tagList( |
||
| 59 | -+ | |||
| 188 | +16x |
- #' - `filter_panel_api` (optional) When provided, the module will be called with `FilterPanelAPI` object+ tags$span(pluralize(datanames, "Dataset")), |
||
| 60 | -+ | |||
| 189 | +16x |
- #' as the value of this argument. (See [`teal.slice::FilterPanelAPI`]).+ tags$span("available in data:"),
|
||
| 61 | -+ | |||
| 190 | +16x |
- #' - `...` (optional) When provided, `server_args` elements will be passed to the module named argument+ tagList( |
||
| 62 | -+ | |||
| 191 | +16x |
- #' or to the `...`.+ tags$span( |
||
| 63 | -+ | |||
| 192 | +16x |
- #' @param ui (`function`) `shiny` UI module function with following arguments:+ to_html_code_list(datanames), |
||
| 64 | -+ | |||
| 193 | +16x |
- #' - `id` - `teal` will set proper `shiny` namespace for this module.+ tags$span(".", .noWS = "outside"),
|
||
| 65 | -+ | |||
| 194 | +16x |
- #' - `...` (optional) When provided, `ui_args` elements will be passed to the module named argument+ .noWS = c("outside")
|
||
| 66 | +195 |
- #' or to the `...`.+ ) |
||
| 67 | +196 |
- #' @param filters (`character`) Deprecated. Use `datanames` instead.+ ) |
||
| 68 | +197 |
- #' @param datanames (`character`) Names of the datasets relevant to the item.+ ) |
||
| 69 | +198 |
- #' There are 2 reserved values that have specific behaviors:+ } else {
|
||
| 70 | -+ | |||
| 199 | +2x |
- #' - The keyword `"all"` includes all datasets available in the data passed to the teal application.+ tags$span("No datasets are available in data.")
|
||
| 71 | +200 |
- #' - `NULL` hides the sidebar panel completely.+ }, |
||
| 72 | -+ | |||
| 201 | +18x |
- #' - If `transformators` are specified, their `datanames` are automatically added to this `datanames`+ tags$br(.noWS = "before") |
||
| 73 | +202 |
- #' argument.+ ) |
||
| 74 | +203 |
- #' @param server_args (named `list`) with additional arguments passed on to the server function.+ } |
||
| 75 | +204 |
- #' @param ui_args (named `list`) with additional arguments passed on to the UI function.+ ) |
||
| 76 | +205 |
- #' @param x (`teal_module` or `teal_modules`) Object to format/print.+ ) |
||
| 77 | +206 |
- #' @param transformators (`list` of `teal_transform_module`) that will be applied to transformator module's data input.+ } |
||
| 78 | +207 |
- #'+ |
||
| 79 | +208 |
- #'+ #' Recursively checks modules and returns list for every datanames mismatch between module and data |
||
| 80 | +209 |
- #' @param ...+ #' @noRd |
||
| 81 | +210 |
- #' - For `modules()`: (`teal_module` or `teal_modules`) Objects to wrap into a tab.+ check_modules_datanames_recursive <- function(modules, datanames) { # nolint: object_name_length
|
||
| 82 | -+ | |||
| 211 | +296x |
- #' - For `format()` and `print()`: Arguments passed to other methods.+ checkmate::assert_multi_class(modules, c("teal_module", "teal_modules"))
|
||
| 83 | -+ | |||
| 212 | +296x |
- #'+ checkmate::assert_character(datanames) |
||
| 84 | -+ | |||
| 213 | +296x |
- #' @return+ if (inherits(modules, "teal_modules")) {
|
||
| 85 | -+ | |||
| 214 | +86x |
- #' `module()` returns an object of class `teal_module`.+ unlist( |
||
| 86 | -+ | |||
| 215 | +86x |
- #'+ lapply(modules$children, check_modules_datanames_recursive, datanames = datanames), |
||
| 87 | -+ | |||
| 216 | +86x |
- #' `modules()` returns a `teal_modules` object which contains following fields:+ recursive = FALSE |
||
| 88 | +217 |
- #' - `label`: taken from the `label` argument.+ ) |
||
| 89 | +218 |
- #' - `children`: a list containing objects passed in `...`. List elements are named after+ } else {
|
||
| 90 | -+ | |||
| 219 | +210x |
- #' their `label` attribute converted to a valid `shiny` id.+ missing_datanames <- setdiff(modules$datanames, c("all", datanames))
|
||
| 91 | -+ | |||
| 220 | +210x |
- #'+ if (length(missing_datanames)) {
|
||
| 92 | -+ | |||
| 221 | +18x |
- #' @name teal_modules+ list(list( |
||
| 93 | -+ | |||
| 222 | +18x |
- #' @aliases teal_module+ label = modules$label, |
||
| 94 | -+ | |||
| 223 | +18x |
- #'+ missing_datanames = missing_datanames |
||
| 95 | +224 |
- #' @examples+ )) |
||
| 96 | +225 |
- #' library(shiny)+ } |
||
| 97 | +226 |
- #'+ } |
||
| 98 | +227 |
- #' module_1 <- module(+ } |
||
| 99 | +228 |
- #' label = "a module",+ |
||
| 100 | +229 |
- #' server = function(id, data) {
+ #' Convert character vector to html code separated with commas and "and" |
||
| 101 | +230 |
- #' moduleServer(+ #' @noRd |
||
| 102 | +231 |
- #' id,+ to_html_code_list <- function(x) {
|
||
| 103 | -+ | |||
| 232 | +40x |
- #' module = function(input, output, session) {
+ checkmate::assert_character(x) |
||
| 104 | -+ | |||
| 233 | +40x |
- #' output$data <- renderDataTable(data()[["iris"]])+ do.call( |
||
| 105 | -+ | |||
| 234 | +40x |
- #' }+ tagList, |
||
| 106 | -+ | |||
| 235 | +40x |
- #' )+ lapply(seq_along(x), function(.ix) {
|
||
| 107 | -+ | |||
| 236 | +56x |
- #' },+ tagList( |
||
| 108 | -+ | |||
| 237 | +56x |
- #' ui = function(id) {
+ tags$code(x[.ix]), |
||
| 109 | -+ | |||
| 238 | +56x |
- #' ns <- NS(id)+ if (.ix != length(x)) {
|
||
| 110 | -+ | |||
| 239 | +1x |
- #' tagList(dataTableOutput(ns("data")))
+ if (.ix == length(x) - 1) tags$span(" and ") else tags$span(", ", .noWS = "before")
|
||
| 111 | +240 |
- #' },+ } |
||
| 112 | +241 |
- #' datanames = "all"+ ) |
||
| 113 | +242 |
- #' )+ }) |
||
| 114 | +243 |
- #'+ ) |
||
| 115 | +244 |
- #' module_2 <- module(+ } |
||
| 116 | +245 |
- #' label = "another module",+ |
||
| 117 | +246 |
- #' server = function(id) {
+
|
||
| 118 | +247 |
- #' moduleServer(+ #' Check `datanames` in filters |
||
| 119 | +248 |
- #' id,+ #' |
||
| 120 | +249 |
- #' module = function(input, output, session) {
+ #' This function checks whether `datanames` in filters correspond to those in `data`, |
||
| 121 | +250 |
- #' output$text <- renderText("Another Module")
+ #' returning character vector with error messages or `TRUE` if all checks pass. |
||
| 122 | +251 |
- #' }+ #' |
||
| 123 | +252 |
- #' )+ #' @param filters (`teal_slices`) object |
||
| 124 | +253 |
- #' },+ #' @param datanames (`character`) names of datasets available in the `data` object |
||
| 125 | +254 |
- #' ui = function(id) {
+ #' |
||
| 126 | +255 |
- #' ns <- NS(id)+ #' @return A `character(1)` containing error message or TRUE if validation passes. |
||
| 127 | +256 |
- #' tagList(textOutput(ns("text")))
+ #' @keywords internal |
||
| 128 | +257 |
- #' },+ check_filter_datanames <- function(filters, datanames) {
|
||
| 129 | -+ | |||
| 258 | +86x |
- #' datanames = NULL+ checkmate::assert_class(filters, "teal_slices") |
||
| 130 | -+ | |||
| 259 | +86x |
- #' )+ checkmate::assert_character(datanames) |
||
| 131 | +260 |
- #'+ |
||
| 132 | +261 |
- #' modules <- modules(+ # check teal_slices against datanames |
||
| 133 | -+ | |||
| 262 | +86x |
- #' label = "modules",+ out <- unlist(sapply( |
||
| 134 | -+ | |||
| 263 | +86x |
- #' modules(+ filters, function(filter) {
|
||
| 135 | -+ | |||
| 264 | +24x |
- #' label = "nested modules",+ dataname <- shiny::isolate(filter$dataname) |
||
| 136 | -+ | |||
| 265 | +24x |
- #' module_1+ if (!dataname %in% datanames) {
|
||
| 137 | -+ | |||
| 266 | +3x |
- #' ),+ sprintf( |
||
| 138 | -+ | |||
| 267 | +3x |
- #' module_2+ "- Filter '%s' refers to dataname not available in 'data':\n %s not in (%s)", |
||
| 139 | -+ | |||
| 268 | +3x |
- #' )+ shiny::isolate(filter$id), |
||
| 140 | -+ | |||
| 269 | +3x |
- #'+ dQuote(dataname, q = FALSE), |
||
| 141 | -+ | |||
| 270 | +3x |
- #' app <- init(+ toString(dQuote(datanames, q = FALSE)) |
||
| 142 | +271 |
- #' data = teal_data(iris = iris),+ ) |
||
| 143 | +272 |
- #' modules = modules+ } |
||
| 144 | +273 |
- #' )+ } |
||
| 145 | +274 |
- #'+ )) |
||
| 146 | +275 |
- #' if (interactive()) {
+
|
||
| 147 | +276 |
- #' shinyApp(app$ui, app$server)+ |
||
| 148 | -+ | |||
| 277 | +86x |
- #' }+ if (length(out)) {
|
||
| 149 | -+ | |||
| 278 | +3x |
- #' @rdname teal_modules+ paste(out, collapse = "\n") |
||
| 150 | +279 |
- #' @export+ } else {
|
||
| 151 | -+ | |||
| 280 | +83x |
- #'+ TRUE |
||
| 152 | +281 |
- module <- function(label = "module",+ } |
||
| 153 | +282 |
- server = function(id, data, ...) moduleServer(id, function(input, output, session) NULL),+ } |
||
| 154 | +283 |
- ui = function(id, ...) tags$p(paste0("This module has no UI (id: ", id, " )")),
+
|
||
| 155 | +284 |
- filters,+ #' Function for validating the title parameter of `teal::init` |
||
| 156 | +285 |
- datanames = "all",+ #' |
||
| 157 | +286 |
- server_args = NULL,+ #' Checks if the input of the title from `teal::init` will create a valid title and favicon tag. |
||
| 158 | +287 |
- ui_args = NULL,+ #' @param shiny_tag (`shiny.tag`) Object to validate for a valid title. |
||
| 159 | +288 |
- transformators = list()) {
+ #' @keywords internal |
||
| 160 | +289 |
- # argument checking (independent)+ validate_app_title_tag <- function(shiny_tag) {
|
||
| 161 | -+ | |||
| 290 | +7x |
- ## `label`+ checkmate::assert_class(shiny_tag, "shiny.tag") |
||
| 162 | -220x | +291 | +7x |
- checkmate::assert_string(label)+ checkmate::assert_true(shiny_tag$name == "head") |
| 163 | -217x | +292 | +6x |
- if (label == "global_filters") {
+ child_names <- vapply(shiny_tag$children, `[[`, character(1L), "name") |
| 164 | -1x | +293 | +6x |
- stop(+ checkmate::assert_subset(c("title", "link"), child_names, .var.name = "child tags")
|
| 165 | -1x | +294 | +4x |
- sprintf("module(label = \"%s\", ...\n ", label),
+ rel_attr <- shiny_tag$children[[which(child_names == "link")]]$attribs$rel |
| 166 | -1x | +295 | +4x |
- "Label 'global_filters' is reserved in teal. Please change to something else.",+ checkmate::assert_subset( |
| 167 | -1x | +296 | +4x |
- call. = FALSE+ rel_attr, |
| 168 | -+ | |||
| 297 | +4x |
- )+ c("icon", "shortcut icon"),
|
||
| 169 | -+ | |||
| 298 | +4x |
- }+ .var.name = "Link tag's rel attribute", |
||
| 170 | -216x | +299 | +4x |
- if (label == "Report previewer") {
+ empty.ok = FALSE |
| 171 | -! | +|||
| 300 | +
- stop(+ ) |
|||
| 172 | -! | +|||
| 301 | +
- sprintf("module(label = \"%s\", ...\n ", label),
+ } |
|||
| 173 | -! | +|||
| 302 | +
- "Label 'Report previewer' is reserved in teal. Please change to something else.",+ |
|||
| 174 | -! | +|||
| 303 | +
- call. = FALSE+ #' Build app title with favicon |
|||
| 175 | +304 |
- )+ #' |
||
| 176 | +305 |
- }+ #' A helper function to create the browser title along with a logo. |
||
| 177 | +306 |
-
+ #' |
||
| 178 | +307 |
- ## server+ #' @param title (`character`) The browser title for the `teal` app. |
||
| 179 | -216x | +|||
| 308 | +
- checkmate::assert_function(server)+ #' @param favicon (`character`) The path for the icon for the title. |
|||
| 180 | -216x | +|||
| 309 | +
- server_formals <- names(formals(server))+ #' The image/icon path can be remote or the static path accessible by `shiny`, like the `www/` |
|||
| 181 | -216x | +|||
| 310 | +
- if (!(+ #' |
|||
| 182 | -216x | +|||
| 311 | +
- "id" %in% server_formals ||+ #' @return A `shiny.tag` containing the element that adds the title and logo to the `shiny` app. |
|||
| 183 | -216x | +|||
| 312 | +
- all(c("input", "output", "session") %in% server_formals)
+ #' @export |
|||
| 184 | +313 |
- )) {
+ build_app_title <- function( |
||
| 185 | -2x | +|||
| 314 | +
- stop(+ title = "teal app", |
|||
| 186 | -2x | +|||
| 315 | +
- "\nmodule() `server` argument requires a function with following arguments:",+ favicon = "https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/PNG/nest.png") {
|
|||
| 187 | -2x | +316 | +15x |
- "\n - id - `teal` will set proper `shiny` namespace for this module.",+ checkmate::assert_string(title, null.ok = TRUE) |
| 188 | -2x | +317 | +15x |
- "\n - input, output, session (not recommended) - then `shiny::callModule` will be used to call a module.",+ checkmate::assert_string(favicon, null.ok = TRUE) |
| 189 | -2x | +318 | +15x |
- "\n\nFollowing arguments can be used optionaly:",+ tags$head( |
| 190 | -2x | +319 | +15x |
- "\n - `data` - module will receive list of reactive (filtered) data specified in the `filters` argument",+ tags$title(title), |
| 191 | -2x | +320 | +15x |
- "\n - `datasets` - module will receive `FilteredData`. See `help(teal.slice::FilteredData)`",+ tags$link( |
| 192 | -2x | +321 | +15x |
- "\n - `reporter` - module will receive `Reporter`. See `help(teal.reporter::Reporter)`",+ rel = "icon", |
| 193 | -2x | +322 | +15x |
- "\n - `filter_panel_api` - module will receive `FilterPanelAPI`. (See [teal.slice::FilterPanelAPI]).",+ href = favicon, |
| 194 | -2x | +323 | +15x |
- "\n - `...` server_args elements will be passed to the module named argument or to the `...`"+ sizes = "any" |
| 195 | +324 |
) |
||
| 196 | +325 |
- }+ ) |
||
| 197 | +326 | - - | -||
| 198 | -214x | -
- if ("datasets" %in% server_formals) {
- |
- ||
| 199 | -2x | -
- warning(- |
- ||
| 200 | -2x | -
- sprintf("Called from module(label = \"%s\", ...)\n ", label),
- |
- ||
| 201 | -2x | -
- "`datasets` argument in the server is deprecated and will be removed in the next release. ",+ } |
||
| 202 | -2x | +|||
| 327 | +
- "Please use `data` instead.",+ |
|||
| 203 | -2x | +|||
| 328 | +
- call. = FALSE+ #' Application ID |
|||
| 204 | +329 |
- )+ #' |
||
| 205 | +330 |
- }+ #' Creates App ID used to match filter snapshots to application. |
||
| 206 | +331 |
-
+ #' |
||
| 207 | +332 |
- ## UI+ #' Calculate app ID that will be used to stamp filter state snapshots. |
||
| 208 | -214x | +|||
| 333 | +
- checkmate::assert_function(ui)+ #' App ID is a hash of the app's data and modules. |
|||
| 209 | -214x | +|||
| 334 | +
- ui_formals <- names(formals(ui))+ #' See "transferring snapshots" section in ?snapshot. |
|||
| 210 | -214x | +|||
| 335 | +
- if (!"id" %in% ui_formals) {
+ #' |
|||
| 211 | -1x | +|||
| 336 | +
- stop(+ #' @param data (`teal_data` or `teal_data_module`) as accepted by `init` |
|||
| 212 | -1x | +|||
| 337 | +
- "\nmodule() `ui` argument requires a function with following arguments:",+ #' @param modules (`teal_modules`) object as accepted by `init` |
|||
| 213 | -1x | +|||
| 338 | +
- "\n - id - `teal` will set proper `shiny` namespace for this module.",+ #' |
|||
| 214 | -1x | +|||
| 339 | +
- "\n\nFollowing arguments can be used optionally:",+ #' @return A single character string. |
|||
| 215 | -1x | +|||
| 340 | +
- "\n - `...` ui_args elements will be passed to the module argument of the same name or to the `...`"+ #' |
|||
| 216 | +341 |
- )+ #' @keywords internal |
||
| 217 | +342 |
- }+ create_app_id <- function(data, modules) {
|
||
| 218 | -+ | |||
| 343 | +23x |
-
+ checkmate::assert_multi_class(data, c("teal_data", "teal_data_module"))
|
||
| 219 | -213x | +344 | +22x |
- if (any(c("data", "datasets") %in% ui_formals)) {
+ checkmate::assert_class(modules, "teal_modules") |
| 220 | -2x | +|||
| 345 | +
- stop(+ |
|||
| 221 | -2x | +346 | +21x |
- sprintf("Called from module(label = \"%s\", ...)\n ", label),
+ data <- if (inherits(data, "teal_data")) {
|
| 222 | -2x | +347 | +19x |
- "UI with `data` or `datasets` argument is no longer accepted.\n ",+ as.list(data) |
| 223 | -2x | +348 | +21x |
- "If some UI inputs depend on data, please move the logic to your server instead.\n ",+ } else if (inherits(data, "teal_data_module")) {
|
| 224 | +349 | 2x |
- "Possible solutions are renderUI() or updateXyzInput() functions."- |
- |
| 225 | -- |
- )+ deparse1(body(data$server)) |
||
| 226 | +350 |
} |
||
| 227 | -+ | |||
| 351 | +21x |
-
+ modules <- lapply(modules, defunction) |
||
| 228 | +352 |
- ## `filters`+ |
||
| 229 | -211x | -
- if (!missing(filters)) {
- |
- ||
| 230 | -! | +353 | +21x |
- datanames <- filters+ rlang::hash(list(data = data, modules = modules)) |
| 231 | -! | +|||
| 354 | +
- msg <-+ } |
|||
| 232 | -! | +|||
| 355 | +
- "The `filters` argument is deprecated and will be removed in the next release. Please use `datanames` instead."+ |
|||
| 233 | -! | +|||
| 356 | +
- warning(msg)+ #' Go through list and extract bodies of encountered functions as string, recursively. |
|||
| 234 | +357 |
- }+ #' @keywords internal |
||
| 235 | +358 |
-
+ #' @noRd |
||
| 236 | +359 |
- ## `datanames` (also including deprecated `filters`)+ defunction <- function(x) {
|
||
| 237 | -+ | |||
| 360 | +297x |
- # please note a race condition between datanames set when filters is not missing and data arg in server function+ if (is.list(x)) {
|
||
| 238 | -211x | +361 | +121x |
- if (!is.element("data", server_formals) && !is.null(datanames)) {
+ lapply(x, defunction) |
| 239 | -12x | +362 | +176x |
- message(sprintf("module \"%s\" server function takes no data so \"datanames\" will be ignored", label))
+ } else if (is.function(x)) {
|
| 240 | -12x | +363 | +54x |
- datanames <- NULL+ deparse1(body(x)) |
| 241 | +364 |
- }+ } else {
|
||
| 242 | -211x | +365 | +122x |
- checkmate::assert_character(datanames, min.len = 1, null.ok = TRUE, any.missing = FALSE)+ x |
| 243 | +366 |
-
+ } |
||
| 244 | +367 |
- ## `server_args`- |
- ||
| 245 | -210x | -
- checkmate::assert_list(server_args, null.ok = TRUE, names = "named")- |
- ||
| 246 | -208x | -
- srv_extra_args <- setdiff(names(server_args), server_formals)- |
- ||
| 247 | -208x | -
- if (length(srv_extra_args) > 0 && !"..." %in% server_formals) {
+ } |
||
| 248 | -1x | +|||
| 368 | +
- stop(+ |
|||
| 249 | -1x | +|||
| 369 | +
- "\nFollowing `server_args` elements have no equivalent in the formals of the server:\n",+ #' Get unique labels |
|||
| 250 | -1x | +|||
| 370 | +
- paste(paste(" -", srv_extra_args), collapse = "\n"),
+ #' |
|||
| 251 | -1x | +|||
| 371 | +
- "\n\nUpdate the server arguments by including above or add `...`"+ #' Get unique labels for the modules to avoid namespace conflicts. |
|||
| 252 | +372 |
- )+ #' |
||
| 253 | +373 |
- }+ #' @param labels (`character`) vector of labels |
||
| 254 | +374 |
-
+ #' |
||
| 255 | +375 |
- ## `ui_args`+ #' @return (`character`) vector of unique labels |
||
| 256 | -207x | +|||
| 376 | +
- checkmate::assert_list(ui_args, null.ok = TRUE, names = "named")+ #' |
|||
| 257 | -205x | +|||
| 377 | +
- ui_extra_args <- setdiff(names(ui_args), ui_formals)+ #' @keywords internal |
|||
| 258 | -205x | +|||
| 378 | +
- if (length(ui_extra_args) > 0 && !"..." %in% ui_formals) {
+ get_unique_labels <- function(labels) {
|
|||
| 259 | -1x | +379 | +141x |
- stop(+ make.unique(gsub("[^[:alnum:]]", "_", tolower(labels)), sep = "_")
|
| 260 | -1x | +|||
| 380 | +
- "\nFollowing `ui_args` elements have no equivalent in the formals of UI:\n",+ } |
|||
| 261 | -1x | +|||
| 381 | +
- paste(paste(" -", ui_extra_args), collapse = "\n"),
+
|
|||
| 262 | -1x | +|||
| 382 | +
- "\n\nUpdate the UI arguments by including above or add `...`"+ #' Remove ANSI escape sequences from a string |
|||
| 263 | +383 |
- )+ #' @noRd |
||
| 264 | +384 |
- }+ strip_style <- function(string) {
|
||
| 265 | -+ | |||
| 385 | +2x |
-
+ checkmate::assert_string(string) |
||
| 266 | +386 |
- ## `transformators`+ |
||
| 267 | -204x | +387 | +2x |
- if (inherits(transformators, "teal_transform_module")) {
+ gsub( |
| 268 | -1x | +388 | +2x |
- transformators <- list(transformators)+ "(?:(?:\\x{001b}\\[)|\\x{009b})(?:(?:[0-9]{1,3})?(?:(?:;[0-9]{0,3})*)?[A-M|f-m])|\\x{001b}[A-M]",
|
| 269 | +389 |
- }+ "", |
||
| 270 | -204x | +390 | +2x |
- checkmate::assert_list(transformators, types = "teal_transform_module")+ string, |
| 271 | -204x | +391 | +2x |
- transform_datanames <- unlist(lapply(transformators, attr, "datanames"))+ perl = TRUE, |
| 272 | -204x | +392 | +2x |
- combined_datanames <- if (identical(datanames, "all")) {
+ useBytes = TRUE |
| 273 | -151x | +|||
| 393 | +
- "all"+ ) |
|||
| 274 | +394 |
- } else {
+ } |
||
| 275 | -53x | +|||
| 395 | +
- union(datanames, transform_datanames)+ |
|||
| 276 | +396 |
- }+ #' @keywords internal |
||
| 277 | +397 |
-
+ #' @noRd |
||
| 278 | -204x | +398 | +4x |
- structure(+ pasten <- function(...) paste0(..., "\n") |
| 279 | -204x | +|||
| 399 | +
- list(+ |
|||
| 280 | -204x | +|||
| 400 | +
- label = label,+ #' Convert character list to human readable html with commas and "and" |
|||
| 281 | -204x | +|||
| 401 | +
- server = server,+ #' @noRd |
|||
| 282 | -204x | +|||
| 402 | +
- ui = ui,+ paste_datanames_character <- function(x, |
|||
| 283 | -204x | +|||
| 403 | +
- datanames = combined_datanames,+ tags = list(span = shiny::tags$span, code = shiny::tags$code), |
|||
| 284 | -204x | +|||
| 404 | +
- server_args = server_args,+ tagList = shiny::tagList) { # nolint: object_name.
|
|||
| 285 | -204x | +|||
| 405 | +! |
- ui_args = ui_args,+ checkmate::assert_character(x) |
||
| 286 | -204x | +|||
| 406 | +! |
- transformators = transformators+ do.call( |
||
| 287 | -+ | |||
| 407 | +! |
- ),+ tagList, |
||
| 288 | -204x | +|||
| 408 | +! |
- class = "teal_module"+ lapply(seq_along(x), function(.ix) {
|
||
| 289 | -+ | |||
| 409 | +! |
- )+ tagList( |
||
| 290 | -+ | |||
| 410 | +! |
- }+ tags$code(x[.ix]), |
||
| 291 | -+ | |||
| 411 | +! |
-
+ if (.ix != length(x)) {
|
||
| 292 | -+ | |||
| 412 | +! |
- #' @rdname teal_modules+ tags$span(if (.ix == length(x) - 1) " and " else ", ") |
||
| 293 | +413 |
- #' @export+ } |
||
| 294 | +414 |
- #'+ ) |
||
| 295 | +415 |
- modules <- function(..., label = "root") {
+ }) |
||
| 296 | -144x | +|||
| 416 | +
- checkmate::assert_string(label)+ ) |
|||
| 297 | -142x | +|||
| 417 | +
- submodules <- list(...)+ } |
|||
| 298 | -142x | +|||
| 418 | +
- if (any(vapply(submodules, is.character, FUN.VALUE = logical(1)))) {
+
|
|||
| 299 | -2x | +|||
| 419 | +
- stop(+ #' Build datanames error string for error message |
|||
| 300 | -2x | +|||
| 420 | +
- "The only character argument to modules() must be 'label' and it must be named, ",+ #' |
|||
| 301 | -2x | +|||
| 421 | +
- "change modules('lab', ...) to modules(label = 'lab', ...)"
+ #' tags and tagList are overwritten in arguments allowing to create strings for |
|||
| 302 | +422 |
- )+ #' logging purposes |
||
| 303 | +423 |
- }+ #' @noRd |
||
| 304 | +424 |
-
+ build_datanames_error_message <- function(label = NULL, |
||
| 305 | -140x | +|||
| 425 | +
- checkmate::assert_list(submodules, min.len = 1, any.missing = FALSE, types = c("teal_module", "teal_modules"))
+ datanames, |
|||
| 306 | +426 |
- # name them so we can more easily access the children+ extra_datanames, |
||
| 307 | +427 |
- # beware however that the label of the submodules should not be changed as it must be kept synced+ tags = list(span = shiny::tags$span, code = shiny::tags$code), |
||
| 308 | -137x | +|||
| 428 | +
- labels <- vapply(submodules, function(submodule) submodule$label, character(1))+ tagList = shiny::tagList) { # nolint: object_name.
|
|||
| 309 | -137x | +|||
| 429 | +! |
- names(submodules) <- get_unique_labels(labels)+ tags$span( |
||
| 310 | -137x | +|||
| 430 | +! |
- structure(+ tags$span(pluralize(extra_datanames, "Dataset")), |
||
| 311 | -137x | +|||
| 431 | +! |
- list(+ paste_datanames_character(extra_datanames, tags, tagList), |
||
| 312 | -137x | +|||
| 432 | +! |
- label = label,+ tags$span( |
||
| 313 | -137x | +|||
| 433 | +! |
- children = submodules+ sprintf( |
||
| 314 | -+ | |||
| 434 | +! |
- ),+ "%s missing%s", |
||
| 315 | -137x | +|||
| 435 | +! |
- class = "teal_modules"+ pluralize(extra_datanames, "is", "are"), |
||
| 316 | -+ | |||
| 436 | +! |
- )+ if (is.null(label)) "" else sprintf(" for tab '%s'", label)
|
||
| 317 | +437 |
- }+ ) |
||
| 318 | +438 |
-
+ ), |
||
| 319 | -+ | |||
| 439 | +! |
- # printing methods ----+ if (length(datanames) >= 1) {
|
||
| 320 | -+ | |||
| 440 | +! |
-
+ tagList( |
||
| 321 | -+ | |||
| 441 | +! |
- #' @rdname teal_modules+ tags$span(pluralize(datanames, "Dataset")), |
||
| 322 | -+ | |||
| 442 | +! |
- #' @param is_last (`logical(1)`) Whether this is the last item in its parent's children list.+ tags$span("available in data:"),
|
||
| 323 | -+ | |||
| 443 | +! |
- #' Affects the tree branch character used (L- vs |-)+ tagList( |
||
| 324 | -+ | |||
| 444 | +! |
- #' @param parent_prefix (`character(1)`) The prefix inherited from parent nodes,+ tags$span( |
||
| 325 | -+ | |||
| 445 | +! |
- #' used to maintain the tree structure in nested levels+ paste_datanames_character(datanames, tags, tagList), |
||
| 326 | -+ | |||
| 446 | +! |
- #' @param is_root (`logical(1)`) Whether this is the root node of the tree. Only used in+ tags$span(".", .noWS = "outside"),
|
||
| 327 | -+ | |||
| 447 | +! |
- #' format.teal_modules(). Determines whether to show "TEAL ROOT" header+ .noWS = c("outside")
|
||
| 328 | +448 |
- #' @param what (`character`) Specifies which metadata to display.+ ) |
||
| 329 | +449 |
- #' Possible values: "datasets", "properties", "ui_args", "server_args", "transformators"+ ) |
||
| 330 | +450 |
- #' @examples+ ) |
||
| 331 | +451 |
- #' mod <- module(+ } else {
|
||
| 332 | -+ | |||
| 452 | +! |
- #' label = "My Custom Module",+ tags$span("No datasets are available in data.")
|
||
| 333 | +453 |
- #' server = function(id, data, ...) {},
+ } |
||
| 334 | +454 |
- #' ui = function(id, ...) {},
+ ) |
||
| 335 | +455 |
- #' datanames = c("ADSL", "ADTTE"),
+ } |
||
| 336 | +456 |
- #' transformators = list(),+ |
||
| 337 | +457 |
- #' ui_args = list(a = 1, b = "b"),+ #' Smart `rbind` |
||
| 338 | +458 |
- #' server_args = list(x = 5, y = list(p = 1))+ #' |
||
| 339 | +459 |
- #' )+ #' Combine `data.frame` objects which have different columns |
||
| 340 | +460 |
- #' cat(format(mod))+ #' |
||
| 341 | +461 |
- #' @export+ #' @param ... (`data.frame`) |
||
| 342 | +462 |
- format.teal_module <- function(+ #' @keywords internal |
||
| 343 | +463 |
- x, is_last = FALSE, parent_prefix = "",+ .smart_rbind <- function(...) {
|
||
| 344 | -+ | |||
| 464 | +89x |
- what = c("datasets", "properties", "ui_args", "server_args", "transformators"), ...) {
+ dots <- list(...) |
||
| 345 | -3x | +465 | +89x |
- empty_text <- ""+ checkmate::assert_list(dots, "data.frame", .var.name = "...") |
| 346 | -3x | +466 | +89x |
- branch <- if (is_last) "L-" else "|-"+ Reduce( |
| 347 | -3x | +467 | +89x |
- current_prefix <- paste0(parent_prefix, branch, " ")+ x = dots, |
| 348 | -3x | +468 | +89x |
- content_prefix <- paste0(parent_prefix, if (is_last) " " else "| ")+ function(x, y) {
|
| 349 | -+ | |||
| 469 | +72x |
-
+ all_columns <- union(colnames(x), colnames(y)) |
||
| 350 | -3x | +470 | +72x |
- format_list <- function(lst, empty = empty_text, label_width = 0) {
+ x[setdiff(all_columns, colnames(x))] <- NA |
| 351 | -6x | +471 | +72x |
- if (is.null(lst) || length(lst) == 0) {
+ y[setdiff(all_columns, colnames(y))] <- NA |
| 352 | -6x | +472 | +72x |
- empty+ rbind(x, y) |
| 353 | +473 |
- } else {
+ } |
||
| 354 | -! | +|||
| 474 | +
- colon_space <- paste(rep(" ", label_width), collapse = "")
+ ) |
|||
| 355 | +475 | ++ |
+ }+ |
+ |
| 476 | ||||
| 356 | -! | +|||
| 477 | +
- first_item <- sprintf("%s (%s)", names(lst)[1], crayon::silver(class(lst[[1]])[1]))
+ #' Pluralize a word depending on the size of the input |
|||
| 357 | -! | +|||
| 478 | +
- rest_items <- if (length(lst) > 1) {
+ #' |
|||
| 358 | -! | +|||
| 479 | +
- paste(+ #' @param x (`object`) to check length for plural. |
|||
| 359 | -! | +|||
| 480 | +
- vapply(+ #' @param singular (`character`) singular form of the word. |
|||
| 360 | -! | +|||
| 481 | +
- names(lst)[-1],+ #' @param plural (optional `character`) plural form of the word. If not given an "s" |
|||
| 361 | -! | +|||
| 482 | +
- function(name) {
+ #' is added to the singular form. |
|||
| 362 | -! | +|||
| 483 | +
- sprintf(+ #' |
|||
| 363 | -! | +|||
| 484 | +
- "%s%s (%s)",+ #' @return A `character` that correctly represents the size of the `x` argument. |
|||
| 364 | -! | +|||
| 485 | +
- paste0(content_prefix, "| ", colon_space),+ #' @keywords internal |
|||
| 365 | -! | +|||
| 486 | +
- name,+ pluralize <- function(x, singular, plural = NULL) {
|
|||
| 366 | -! | +|||
| 487 | +70x |
- crayon::silver(class(lst[[name]])[1])+ checkmate::assert_string(singular) |
||
| 367 | -+ | |||
| 488 | +70x |
- )+ checkmate::assert_string(plural, null.ok = TRUE) |
||
| 368 | -+ | |||
| 489 | +70x |
- },+ if (length(x) == 1L) { # Zero length object should use plural form.
|
||
| 369 | -! | +|||
| 490 | +42x |
- character(1)+ singular |
||
| 370 | +491 |
- ),+ } else {
|
||
| 371 | -! | +|||
| 492 | +28x |
- collapse = "\n"+ if (is.null(plural)) {
|
||
| 372 | -+ | |||
| 493 | +12x |
- )+ sprintf("%ss", singular)
|
||
| 373 | +494 |
- }+ } else {
|
||
| 374 | -! | +|||
| 495 | +16x |
- if (length(lst) > 1) paste0(first_item, "\n", rest_items) else first_item+ plural |
||
| 375 | +496 |
} |
||
| 376 | +497 |
} |
||
| 377 | +498 | ++ |
+ }+ |
+
| 1 | ++ |
+ #' Data Module for teal+ |
+ ||
| 2 |
-
+ #' |
|||
| 378 | -3x | +|||
| 3 | +
- bookmarkable <- isTRUE(attr(x, "teal_bookmarkable"))+ #' This module manages the `data` argument for `srv_teal`. The `teal` framework uses [teal.data::teal_data()], |
|||
| 379 | -3x | +|||
| 4 | +
- reportable <- "reporter" %in% names(formals(x$server))+ #' which can be provided in various ways: |
|||
| 380 | +5 |
-
+ #' 1. Directly as a [teal.data::teal_data()] object. This will automatically convert it into a `reactive` `teal_data`. |
||
| 381 | -3x | +|||
| 6 | +
- transformators <- if (length(x$transformators) > 0) {
+ #' 2. As a `reactive` object that returns a [teal.data::teal_data()] object. |
|||
| 382 | -! | +|||
| 7 | +
- paste(sapply(x$transformators, function(t) attr(t, "label")), collapse = ", ")+ #' |
|||
| 383 | +8 |
- } else {
+ #' @details |
||
| 384 | -3x | +|||
| 9 | +
- empty_text+ #' ## Reactive `teal_data`: |
|||
| 385 | +10 |
- }+ #' |
||
| 386 | +11 |
-
+ #' The data in the application can be reactively updated, prompting [srv_teal()] to rebuild the |
||
| 387 | -3x | +|||
| 12 | +
- output <- pasten(current_prefix, crayon::bgWhite(x$label))+ #' content accordingly. There are two methods for creating interactive `teal_data`: |
|||
| 388 | +13 |
-
+ #' 1. Using a `reactive` object provided from outside the `teal` application. In this scenario, |
||
| 389 | -3x | +|||
| 14 | +
- if ("datasets" %in% what) {
+ #' reactivity is controlled by an external module, and `srv_teal` responds to changes. |
|||
| 390 | -3x | +|||
| 15 | +
- output <- paste0(+ #' 2. Using [teal_data_module()], which is embedded within the `teal` application, allowing data to |
|||
| 391 | -3x | +|||
| 16 | +
- output,+ #' be resubmitted by the user as needed. |
|||
| 392 | -3x | +|||
| 17 | +
- content_prefix, "|- ", crayon::yellow("Datasets : "), paste(x$datanames, collapse = ", "), "\n"
+ #' |
|||
| 393 | +18 |
- )+ #' Since the server of [teal_data_module()] must return a `reactive` `teal_data` object, both |
||
| 394 | +19 |
- }+ #' methods (1 and 2) produce the same reactive behavior within a `teal` application. The distinction |
||
| 395 | -3x | +|||
| 20 | +
- if ("properties" %in% what) {
+ #' lies in data control: the first method involves external control, while the second method |
|||
| 396 | -3x | +|||
| 21 | +
- output <- paste0(+ #' involves control from a custom module within the app. |
|||
| 397 | -3x | +|||
| 22 | +
- output,+ #' |
|||
| 398 | -3x | +|||
| 23 | +
- content_prefix, "|- ", crayon::blue("Properties:"), "\n",
+ #' For more details, see [`module_teal_data`]. |
|||
| 399 | -3x | +|||
| 24 | +
- content_prefix, "| |- ", crayon::cyan("Bookmarkable : "), bookmarkable, "\n",
+ #' |
|||
| 400 | -3x | +|||
| 25 | +
- content_prefix, "| L- ", crayon::cyan("Reportable : "), reportable, "\n"
+ #' @inheritParams init |
|||
| 401 | +26 |
- )+ #' |
||
| 402 | +27 |
- }+ #' @param data (`teal_data`, `teal_data_module`, or `reactive` returning `teal_data`) |
||
| 403 | -3x | +|||
| 28 | +
- if ("ui_args" %in% what) {
+ #' The data which application will depend on. |
|||
| 404 | -3x | +|||
| 29 | +
- ui_args_formatted <- format_list(x$ui_args, label_width = 19)+ #' |
|||
| 405 | -3x | +|||
| 30 | +
- output <- paste0(+ #' @return A `reactive` object that returns: |
|||
| 406 | -3x | +|||
| 31 | +
- output,+ #' Output of the `data`. If `data` fails then returned error is handled (after [tryCatch()]) so that |
|||
| 407 | -3x | +|||
| 32 | +
- content_prefix, "|- ", crayon::green("UI Arguments : "), ui_args_formatted, "\n"
+ #' rest of the application can respond to this respectively. |
|||
| 408 | +33 |
- )+ #' |
||
| 409 | +34 |
- }+ #' @rdname module_init_data |
||
| 410 | -3x | +|||
| 35 | +
- if ("server_args" %in% what) {
+ #' @name module_init_data |
|||
| 411 | -3x | +|||
| 36 | +
- server_args_formatted <- format_list(x$server_args, label_width = 19)+ #' @keywords internal |
|||
| 412 | -3x | +|||
| 37 | +
- output <- paste0(+ NULL |
|||
| 413 | -3x | +|||
| 38 | +
- output,+ |
|||
| 414 | -3x | +|||
| 39 | +
- content_prefix, "|- ", crayon::green("Server Arguments : "), server_args_formatted, "\n"
+ #' @rdname module_init_data |
|||
| 415 | +40 |
- )+ ui_init_data <- function(id) {
|
||
| 416 | -+ | |||
| 41 | +9x |
- }+ ns <- shiny::NS(id) |
||
| 417 | -3x | +42 | +9x |
- if ("transformators" %in% what) {
+ shiny::div( |
| 418 | -3x | +43 | +9x |
- output <- paste0(+ id = ns("content"),
|
| 419 | -3x | +44 | +9x |
- output,+ style = "display: inline-block; width: 100%;", |
| 420 | -3x | +45 | +9x |
- content_prefix, "L- ", crayon::magenta("Transformators : "), transformators, "\n"
+ uiOutput(ns("data"))
|
| 421 | +46 |
- )+ ) |
||
| 422 | +47 |
- }+ } |
||
| 423 | +48 | |||
| 424 | -3x | +|||
| 49 | +
- output+ #' @rdname module_init_data |
|||
| 425 | +50 |
- }+ srv_init_data <- function(id, data) {
|
||
| 426 | -+ | |||
| 51 | +88x |
-
+ checkmate::assert_character(id, max.len = 1, any.missing = FALSE) |
||
| 427 | -+ | |||
| 52 | +88x |
- #' @rdname teal_modules+ checkmate::assert_multi_class(data, c("teal_data", "teal_data_module", "reactive"))
|
||
| 428 | +53 |
- #' @examples+ |
||
| 429 | -+ | |||
| 54 | +88x |
- #' custom_module <- function(+ moduleServer(id, function(input, output, session) {
|
||
| 430 | -+ | |||
| 55 | +88x |
- #' label = "label", ui_args = NULL, server_args = NULL,+ logger::log_debug("srv_data initializing.")
|
||
| 431 | -+ | |||
| 56 | +88x |
- #' datanames = "all", transformators = list(), bk = FALSE) {
+ data_out <- if (inherits(data, "teal_data_module")) {
|
||
| 432 | -+ | |||
| 57 | +10x |
- #' ans <- module(+ output$data <- renderUI(data$ui(id = session$ns("teal_data_module")))
|
||
| 433 | -+ | |||
| 58 | +10x |
- #' label,+ data$server("teal_data_module")
|
||
| 434 | -+ | |||
| 59 | +88x |
- #' server = function(id, data, ...) {},
+ } else if (inherits(data, "teal_data")) {
|
||
| 435 | -+ | |||
| 60 | +48x |
- #' ui = function(id, ...) {
+ reactiveVal(data) |
||
| 436 | -+ | |||
| 61 | +88x |
- #' },+ } else if (test_reactive(data)) {
|
||
| 437 | -+ | |||
| 62 | +30x |
- #' datanames = datanames,+ data |
||
| 438 | +63 |
- #' transformators = transformators,+ } |
||
| 439 | +64 |
- #' ui_args = ui_args,+ |
||
| 440 | -+ | |||
| 65 | +87x |
- #' server_args = server_args+ data_handled <- reactive({
|
||
| 441 | -+ | |||
| 66 | +80x |
- #' )+ tryCatch(data_out(), error = function(e) e) |
||
| 442 | +67 |
- #' attr(ans, "teal_bookmarkable") <- bk+ }) |
||
| 443 | +68 |
- #' ans+ |
||
| 444 | +69 |
- #' }+ # We want to exclude teal_data_module elements from bookmarking as they might have some secrets |
||
| 445 | -+ | |||
| 70 | +87x |
- #'+ observeEvent(data_handled(), {
|
||
| 446 | -+ | |||
| 71 | +80x |
- #' dummy_transformator <- teal_transform_module(+ if (inherits(data_handled(), "teal_data")) {
|
||
| 447 | -+ | |||
| 72 | +75x |
- #' label = "Dummy Transform",+ app_session <- .subset2(shiny::getDefaultReactiveDomain(), "parent") |
||
| 448 | -+ | |||
| 73 | +75x |
- #' ui = function(id) div("(does nothing)"),
+ setBookmarkExclude( |
||
| 449 | -+ | |||
| 74 | +75x |
- #' server = function(id, data) {
+ session$ns( |
||
| 450 | -+ | |||
| 75 | +75x |
- #' moduleServer(id, function(input, output, session) data)+ grep( |
||
| 451 | -+ | |||
| 76 | +75x |
- #' }+ pattern = "teal_data_module-", |
||
| 452 | -+ | |||
| 77 | +75x |
- #' )+ x = names(reactiveValuesToList(input)), |
||
| 453 | -+ | |||
| 78 | +75x |
- #'+ value = TRUE |
||
| 454 | +79 |
- #' plot_transformator <- teal_transform_module(+ ) |
||
| 455 | +80 |
- #' label = "Plot Settings",+ ), |
||
| 456 | -+ | |||
| 81 | +75x |
- #' ui = function(id) div("(does nothing)"),
+ session = app_session |
||
| 457 | +82 |
- #' server = function(id, data) {
+ ) |
||
| 458 | +83 |
- #' moduleServer(id, function(input, output, session) data)+ } |
||
| 459 | +84 |
- #' }+ }) |
||
| 460 | +85 |
- #' )+ |
||
| 461 | -+ | |||
| 86 | +87x |
- #'+ data_handled |
||
| 462 | +87 |
- #' complete_modules <- modules(+ }) |
||
| 463 | +88 |
- #' custom_module(+ } |
||
| 464 | +89 |
- #' label = "Data Overview",+ |
||
| 465 | +90 |
- #' datanames = c("ADSL", "ADAE", "ADVS"),
+ #' Adds signature protection to the `datanames` in the data |
||
| 466 | +91 |
- #' ui_args = list(+ #' @param data (`teal_data`) |
||
| 467 | +92 |
- #' view_type = "table",+ #' @return `teal_data` with additional code that has signature of the `datanames` |
||
| 468 | +93 |
- #' page_size = 10,+ #' @keywords internal |
||
| 469 | +94 |
- #' filters = c("ARM", "SEX", "RACE")
+ .add_signature_to_data <- function(data) {
|
||
| 470 | -+ | |||
| 95 | +75x |
- #' ),+ hashes <- .get_hashes_code(data) |
||
| 471 | -+ | |||
| 96 | +75x |
- #' server_args = list(+ tdata <- do.call( |
||
| 472 | -+ | |||
| 97 | +75x |
- #' cache = TRUE,+ teal.data::teal_data, |
||
| 473 | -+ | |||
| 98 | +75x |
- #' debounce = 1000+ c( |
||
| 474 | -+ | |||
| 99 | +75x |
- #' ),+ list(code = trimws(c(teal.code::get_code(data), hashes), which = "right")), |
||
| 475 | -+ | |||
| 100 | +75x |
- #' transformators = list(dummy_transformator),+ list(join_keys = teal.data::join_keys(data)), |
||
| 476 | -+ | |||
| 101 | +75x |
- #' bk = TRUE+ sapply( |
||
| 477 | -+ | |||
| 102 | +75x |
- #' ),+ names(data), |
||
| 478 | -+ | |||
| 103 | +75x |
- #' modules(+ teal.code::get_var, |
||
| 479 | -+ | |||
| 104 | +75x |
- #' label = "Nested 1",+ object = data, |
||
| 480 | -+ | |||
| 105 | +75x |
- #' custom_module(+ simplify = FALSE |
||
| 481 | +106 |
- #' label = "Interactive Plots",+ ) |
||
| 482 | +107 |
- #' datanames = c("ADSL", "ADVS"),
+ ) |
||
| 483 | +108 |
- #' ui_args = list(+ ) |
||
| 484 | +109 |
- #' plot_type = c("scatter", "box", "line"),
+
|
||
| 485 | -+ | |||
| 110 | +75x |
- #' height = 600,+ tdata@verified <- data@verified |
||
| 486 | -+ | |||
| 111 | +75x |
- #' width = 800,+ tdata |
||
| 487 | +112 |
- #' color_scheme = "viridis"+ } |
||
| 488 | +113 |
- #' ),+ |
||
| 489 | +114 |
- #' server_args = list(+ #' Get code that tests the integrity of the reproducible data |
||
| 490 | +115 |
- #' render_type = "svg",+ #' |
||
| 491 | +116 |
- #' cache_plots = TRUE+ #' @param data (`teal_data`) object holding the data |
||
| 492 | +117 |
- #' ),+ #' @param datanames (`character`) names of `datasets` |
||
| 493 | +118 |
- #' transformators = list(dummy_transformator, plot_transformator),+ #' |
||
| 494 | +119 |
- #' bk = TRUE+ #' @return A character vector with the code lines. |
||
| 495 | +120 |
- #' ),+ #' @keywords internal |
||
| 496 | +121 |
- #' modules(+ #' |
||
| 497 | +122 |
- #' label = "Nested 2",+ .get_hashes_code <- function(data, datanames = names(data)) {
|
||
| 498 | -+ | |||
| 123 | +75x |
- #' custom_module(+ vapply( |
||
| 499 | -+ | |||
| 124 | +75x |
- #' label = "Summary Statistics",+ datanames, |
||
| 500 | -+ | |||
| 125 | +75x |
- #' datanames = "ADSL",+ function(dataname, datasets) {
|
||
| 501 | -+ | |||
| 126 | +133x |
- #' ui_args = list(+ x <- data[[dataname]] |
||
| 502 | +127 |
- #' stats = c("mean", "median", "sd", "range"),
+
|
||
| 503 | -+ | |||
| 128 | +133x |
- #' grouping = c("ARM", "SEX")
+ code <- if (is.function(x) && !is.primitive(x)) {
|
||
| 504 | -+ | |||
| 129 | +6x |
- #' )+ x <- deparse1(x) |
||
| 505 | -+ | |||
| 130 | +6x |
- #' ),+ bquote(rlang::hash(deparse1(.(as.name(dataname))))) |
||
| 506 | +131 |
- #' modules(+ } else {
|
||
| 507 | -+ | |||
| 132 | +127x |
- #' label = "Labeled nested modules",+ bquote(rlang::hash(.(as.name(dataname)))) |
||
| 508 | +133 |
- #' custom_module(+ } |
||
| 509 | -+ | |||
| 134 | +133x |
- #' label = "Subgroup Analysis",+ sprintf( |
||
| 510 | -+ | |||
| 135 | +133x |
- #' datanames = c("ADSL", "ADAE"),
+ "stopifnot(%s == %s) # @linksto %s", |
||
| 511 | -+ | |||
| 136 | +133x |
- #' ui_args = list(+ deparse1(code), |
||
| 512 | -+ | |||
| 137 | +133x |
- #' subgroups = c("AGE", "SEX", "RACE"),
+ deparse1(rlang::hash(x)), |
||
| 513 | -+ | |||
| 138 | +133x |
- #' analysis_type = "stratified"+ dataname |
||
| 514 | +139 |
- #' ),+ ) |
||
| 515 | +140 |
- #' bk = TRUE+ }, |
||
| 516 | -+ | |||
| 141 | +75x |
- #' )+ character(1L), |
||
| 517 | -+ | |||
| 142 | +75x |
- #' ),+ USE.NAMES = TRUE |
||
| 518 | +143 |
- #' modules(custom_module(label = "Subgroup Analysis in non-labled modules"))+ ) |
||
| 519 | +144 |
- #' )+ } |
| 520 | +1 |
- #' ),+ # This is the main function from teal to be used by the end-users. Although it delegates |
||
| 521 | +2 |
- #' custom_module("Non-nested module")
+ # directly to `module_teal_with_splash.R`, we keep it in a separate file because its documentation is quite large |
||
| 522 | +3 |
- #' )+ # and it is very end-user oriented. It may also perform more argument checking with more informative |
||
| 523 | +4 |
- #'+ # error messages. |
||
| 524 | +5 |
- #' cat(format(complete_modules))+ |
||
| 525 | +6 |
- #' cat(format(complete_modules, what = c("ui_args", "server_args", "transformators")))
+ #' Create the server and UI function for the `shiny` app |
||
| 526 | +7 |
- #' @export+ #' |
||
| 527 | +8 |
- format.teal_modules <- function(x, is_root = TRUE, is_last = FALSE, parent_prefix = "", ...) {
- |
- ||
| 528 | -1x | -
- if (is_root) {
+ #' @description `r lifecycle::badge("stable")`
|
||
| 529 | -1x | +|||
| 9 | +
- header <- pasten(crayon::bold("TEAL ROOT"))
+ #' |
|||
| 530 | -1x | +|||
| 10 | +
- new_parent_prefix <- " " #' Initial indent for root level+ #' End-users: This is the most important function for you to start a |
|||
| 531 | +11 |
- } else {
+ #' `teal` app that is composed of `teal` modules. |
||
| 532 | -! | +|||
| 12 | +
- if (!is.null(x$label)) {
+ #' |
|||
| 533 | -! | +|||
| 13 | +
- branch <- if (is_last) "L-" else "|-"+ #' @param data (`teal_data` or `teal_data_module`) |
|||
| 534 | -! | +|||
| 14 | +
- header <- pasten(parent_prefix, branch, " ", crayon::bold(x$label))+ #' For constructing the data object, refer to [teal.data::teal_data()] and [teal_data_module()]. |
|||
| 535 | -! | +|||
| 15 | +
- new_parent_prefix <- paste0(parent_prefix, if (is_last) " " else "| ")+ #' If `datanames` are not set for the `teal_data` object, defaults from the `teal_data` environment will be used. |
|||
| 536 | +16 |
- } else {
+ #' @param modules (`list` or `teal_modules` or `teal_module`) |
||
| 537 | -! | +|||
| 17 | +
- header <- ""+ #' Nested list of `teal_modules` or `teal_module` objects or a single |
|||
| 538 | -! | +|||
| 18 | +
- new_parent_prefix <- parent_prefix+ #' `teal_modules` or `teal_module` object. These are the specific output modules which |
|||
| 539 | +19 |
- }+ #' will be displayed in the `teal` application. See [modules()] and [module()] for |
||
| 540 | +20 |
- }+ #' more details. |
||
| 541 | +21 |
-
+ #' @param filter (`teal_slices`) Optionally, |
||
| 542 | -1x | +|||
| 22 | +
- if (length(x$children) > 0) {
+ #' specifies the initial filter using [teal_slices()]. |
|||
| 543 | -1x | +|||
| 23 | +
- children_output <- character(0)+ #' @param title (`shiny.tag` or `character(1)`) Optionally, |
|||
| 544 | -1x | +|||
| 24 | +
- n_children <- length(x$children)+ #' the browser window title. Defaults to a title "teal app" with the icon of NEST. |
|||
| 545 | +25 |
-
+ #' Can be created using the `build_app_title()` or |
||
| 546 | -1x | +|||
| 26 | +
- for (i in seq_along(x$children)) {
+ #' by passing a valid `shiny.tag` which is a head tag with title and link tag. |
|||
| 547 | -3x | +|||
| 27 | +
- child <- x$children[[i]]+ #' @param header (`shiny.tag` or `character(1)`) Optionally, |
|||
| 548 | -3x | +|||
| 28 | +
- is_last_child <- (i == n_children)+ #' the header of the app. |
|||
| 549 | +29 |
-
+ #' @param footer (`shiny.tag` or `character(1)`) Optionally, |
||
| 550 | -3x | +|||
| 30 | +
- if (inherits(child, "teal_modules")) {
+ #' the footer of the app. |
|||
| 551 | -! | +|||
| 31 | +
- children_output <- c(+ #' @param id (`character`) Optionally, |
|||
| 552 | -! | +|||
| 32 | +
- children_output,+ #' a string specifying the `shiny` module id in cases it is used as a `shiny` module |
|||
| 553 | -! | +|||
| 33 | +
- format(child,+ #' rather than a standalone `shiny` app. This is a legacy feature. |
|||
| 554 | -! | +|||
| 34 | +
- is_root = FALSE,+ #' @param landing_popup (`teal_module_landing`) Optionally, |
|||
| 555 | -! | +|||
| 35 | +
- is_last = is_last_child,+ #' a `landing_popup_module` to show up as soon as the teal app is initialized. |
|||
| 556 | -! | +|||
| 36 | +
- parent_prefix = new_parent_prefix,+ #' |
|||
| 557 | +37 |
- ...+ #' @return Named list containing server and UI functions. |
||
| 558 | +38 |
- )+ #' |
||
| 559 | +39 |
- )+ #' @export |
||
| 560 | +40 |
- } else {
+ #' |
||
| 561 | -3x | +|||
| 41 | +
- children_output <- c(+ #' @include modules.R |
|||
| 562 | -3x | +|||
| 42 | +
- children_output,+ #' |
|||
| 563 | -3x | +|||
| 43 | +
- format(child,+ #' @examples |
|||
| 564 | -3x | +|||
| 44 | +
- is_last = is_last_child,+ #' app <- init( |
|||
| 565 | -3x | +|||
| 45 | +
- parent_prefix = new_parent_prefix,+ #' data = within( |
|||
| 566 | +46 |
- ...+ #' teal_data(), |
||
| 567 | +47 |
- )+ #' {
|
||
| 568 | +48 |
- )+ #' new_iris <- transform(iris, id = seq_len(nrow(iris))) |
||
| 569 | +49 |
- }+ #' new_mtcars <- transform(mtcars, id = seq_len(nrow(mtcars))) |
||
| 570 | +50 |
- }+ #' } |
||
| 571 | +51 |
-
+ #' ), |
||
| 572 | -1x | +|||
| 52 | +
- paste0(header, paste(children_output, collapse = ""))+ #' modules = modules( |
|||
| 573 | +53 |
- } else {
+ #' module( |
||
| 574 | -! | +|||
| 54 | +
- header+ #' label = "data source", |
|||
| 575 | +55 |
- }+ #' server = function(input, output, session, data) {},
|
||
| 576 | +56 |
- }+ #' ui = function(id, ...) tags$div(p("information about data source")),
|
||
| 577 | +57 |
-
+ #' datanames = "all" |
||
| 578 | +58 |
- #' @rdname teal_modules+ #' ), |
||
| 579 | +59 |
- #' @export+ #' example_module(label = "example teal module"), |
||
| 580 | +60 |
- print.teal_module <- function(x, ...) {
+ #' module( |
||
| 581 | -! | +|||
| 61 | +
- cat(format(x, ...))+ #' "Iris Sepal.Length histogram", |
|||
| 582 | -! | +|||
| 62 | +
- invisible(x)+ #' server = function(input, output, session, data) {
|
|||
| 583 | +63 |
- }+ #' output$hist <- renderPlot( |
||
| 584 | +64 |
-
+ #' hist(data()[["new_iris"]]$Sepal.Length) |
||
| 585 | +65 |
- #' @rdname teal_modules+ #' ) |
||
| 586 | +66 |
- #' @export+ #' }, |
||
| 587 | +67 |
- print.teal_modules <- function(x, ...) {
+ #' ui = function(id, ...) {
|
||
| 588 | -! | +|||
| 68 | +
- cat(format(x, ...))+ #' ns <- NS(id) |
|||
| 589 | -! | +|||
| 69 | +
- invisible(x)+ #' plotOutput(ns("hist"))
|
|||
| 590 | +70 |
- }+ #' }, |
||
| 591 | +71 |
-
+ #' datanames = "new_iris" |
||
| 592 | +72 |
- #' @param modules (`teal_module` or `teal_modules`)+ #' ) |
||
| 593 | +73 |
- #' @rdname teal_modules+ #' ), |
||
| 594 | +74 |
- #' @examples+ #' filter = teal_slices( |
||
| 595 | +75 |
- #' # change the module's datanames+ #' teal_slice(dataname = "new_iris", varname = "Species"), |
||
| 596 | +76 |
- #' set_datanames(module(datanames = "all"), "a")+ #' teal_slice(dataname = "new_iris", varname = "Sepal.Length"), |
||
| 597 | +77 |
- #'+ #' teal_slice(dataname = "new_mtcars", varname = "cyl"), |
||
| 598 | +78 |
- #' # change modules' datanames+ #' exclude_varnames = list(new_iris = c("Sepal.Width", "Petal.Width")),
|
||
| 599 | +79 |
- #' set_datanames(+ #' module_specific = TRUE, |
||
| 600 | +80 |
- #' modules(+ #' mapping = list( |
||
| 601 | +81 |
- #' module(datanames = "all"),+ #' `example teal module` = "new_iris Species", |
||
| 602 | +82 |
- #' module(datanames = "a")+ #' `Iris Sepal.Length histogram` = "new_iris Species", |
||
| 603 | +83 |
- #' ),+ #' global_filters = "new_mtcars cyl" |
||
| 604 | +84 |
- #' "b"+ #' ) |
||
| 605 | +85 |
- #' )+ #' ), |
||
| 606 | +86 |
- #' @export+ #' title = "App title", |
||
| 607 | +87 |
- set_datanames <- function(modules, datanames) {
+ #' header = tags$h1("Sample App"),
|
||
| 608 | -! | +|||
| 88 | +
- checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"))
+ #' footer = tags$p("Sample footer")
|
|||
| 609 | -! | +|||
| 89 | +
- if (inherits(modules, "teal_modules")) {
+ #' ) |
|||
| 610 | -! | +|||
| 90 | +
- modules$children <- lapply(modules$children, set_datanames, datanames)+ #' if (interactive()) {
|
|||
| 611 | +91 |
- } else {
+ #' shinyApp(app$ui, app$server) |
||
| 612 | -! | +|||
| 92 | +
- if (identical(modules$datanames, "all")) {
+ #' } |
|||
| 613 | -! | +|||
| 93 | +
- modules$datanames <- datanames+ #' |
|||
| 614 | +94 |
- } else {
+ init <- function(data, |
||
| 615 | -! | +|||
| 95 | +
- warning(+ modules, |
|||
| 616 | -! | +|||
| 96 | +
- "Not possible to modify datanames of the module ", modules$label,+ filter = teal_slices(), |
|||
| 617 | -! | +|||
| 97 | +
- ". set_datanames() can only change datanames if it was set to \"all\".",+ title = build_app_title(), |
|||
| 618 | -! | +|||
| 98 | +
- call. = FALSE+ header = tags$p(), |
|||
| 619 | +99 |
- )+ footer = tags$p(), |
||
| 620 | +100 |
- }+ id = character(0), |
||
| 621 | +101 |
- }+ landing_popup = NULL) {
|
||
| 622 | -! | +|||
| 102 | +14x |
- modules+ logger::log_debug("init initializing teal app with: data ('{ class(data) }').")
|
||
| 623 | +103 |
- }+ |
||
| 624 | +104 |
-
+ # argument checking (independent) |
||
| 625 | +105 |
- # utilities ----+ ## `data` |
||
| 626 | -+ | |||
| 106 | +14x |
- ## subset or modify modules ----+ checkmate::assert_multi_class(data, c("teal_data", "teal_data_module"))
+ |
+ ||
| 107 | +14x | +
+ checkmate::assert_class(landing_popup, "teal_module_landing", null.ok = TRUE) |
||
| 627 | +108 | |||
| 628 | +109 |
- #' Append a `teal_module` to `children` of a `teal_modules` object+ ## `modules` |
||
| 629 | -+ | |||
| 110 | +14x |
- #' @keywords internal+ checkmate::assert( |
||
| 630 | -+ | |||
| 111 | +14x |
- #' @param modules (`teal_modules`)+ .var.name = "modules", |
||
| 631 | -+ | |||
| 112 | +14x |
- #' @param module (`teal_module`) object to be appended onto the children of `modules`+ checkmate::check_multi_class(modules, c("teal_modules", "teal_module")),
|
||
| 632 | -+ | |||
| 113 | +14x |
- #' @return A `teal_modules` object with `module` appended.+ checkmate::check_list(modules, min.len = 1, any.missing = FALSE, types = c("teal_module", "teal_modules"))
|
||
| 633 | +114 |
- append_module <- function(modules, module) {
- |
- ||
| 634 | -8x | -
- checkmate::assert_class(modules, "teal_modules")+ ) |
||
| 635 | -6x | +115 | +14x |
- checkmate::assert_class(module, "teal_module")+ if (inherits(modules, "teal_module")) {
|
| 636 | -4x | +116 | +1x |
- modules$children <- c(modules$children, list(module))+ modules <- list(modules) |
| 637 | -4x | +|||
| 117 | +
- labels <- vapply(modules$children, function(submodule) submodule$label, character(1))+ } |
|||
| 638 | -4x | +118 | +14x |
- names(modules$children) <- get_unique_labels(labels)+ if (checkmate::test_list(modules, min.len = 1, any.missing = FALSE, types = c("teal_module", "teal_modules"))) {
|
| 639 | -4x | +119 | +8x |
- modules+ modules <- do.call(teal::modules, modules) |
| 640 | +120 |
- }+ } |
||
| 641 | +121 | |||
| 642 | +122 |
- #' Extract/Remove module(s) of specific class+ ## `filter` |
||
| 643 | -+ | |||
| 123 | +14x |
- #'+ checkmate::assert_class(filter, "teal_slices") |
||
| 644 | +124 |
- #' Given a `teal_module` or a `teal_modules`, return the elements of the structure according to `class`.+ |
||
| 645 | +125 |
- #'+ ## all other arguments |
||
| 646 | -+ | |||
| 126 | +13x |
- #' @param modules (`teal_modules`)+ checkmate::assert( |
||
| 647 | -+ | |||
| 127 | +13x |
- #' @param class The class name of `teal_module` to be extracted or dropped.+ .var.name = "title", |
||
| 648 | -+ | |||
| 128 | +13x |
- #' @keywords internal+ checkmate::check_string(title), |
||
| 649 | -+ | |||
| 129 | +13x |
- #' @return+ checkmate::check_multi_class(title, c("shiny.tag", "shiny.tag.list", "html"))
|
||
| 650 | +130 |
- #' - For `extract_module`, a `teal_module` of class `class` or `teal_modules` containing modules of class `class`.+ ) |
||
| 651 | -+ | |||
| 131 | +13x |
- #' - For `drop_module`, the opposite, which is all `teal_modules` of class other than `class`.+ checkmate::assert( |
||
| 652 | -+ | |||
| 132 | +13x |
- #' @rdname module_management+ .var.name = "header", |
||
| 653 | -+ | |||
| 133 | +13x |
- extract_module <- function(modules, class) {
+ checkmate::check_string(header), |
||
| 654 | -28x | +134 | +13x |
- if (inherits(modules, class)) {
+ checkmate::check_multi_class(header, c("shiny.tag", "shiny.tag.list", "html"))
|
| 655 | -! | +|||
| 135 | +
- modules+ ) |
|||
| 656 | -28x | +136 | +13x |
- } else if (inherits(modules, "teal_module")) {
+ checkmate::assert( |
| 657 | -15x | +137 | +13x |
- NULL+ .var.name = "footer", |
| 658 | +138 | 13x |
- } else if (inherits(modules, "teal_modules")) {
+ checkmate::check_string(footer), |
|
| 659 | +139 | 13x |
- Filter(function(x) length(x) > 0L, lapply(modules$children, extract_module, class))+ checkmate::check_multi_class(footer, c("shiny.tag", "shiny.tag.list", "html"))
|
|
| 660 | +140 |
- }+ ) |
||
| 661 | -+ | |||
| 141 | +13x |
- }+ checkmate::assert_character(id, max.len = 1, any.missing = FALSE) |
||
| 662 | +142 | |||
| 663 | +143 |
- #' @keywords internal+ # log+ |
+ ||
| 144 | +13x | +
+ teal.logger::log_system_info() |
||
| 664 | +145 |
- #' @return `teal_modules`+ |
||
| 665 | +146 |
- #' @rdname module_management+ # argument transformations |
||
| 666 | +147 |
- drop_module <- function(modules, class) {
+ ## `modules` - landing module+ |
+ ||
| 148 | +13x | +
+ landing <- extract_module(modules, "teal_module_landing")+ |
+ ||
| 149 | +13x | +
+ if (length(landing) == 1L) {
|
||
| 667 | +150 | ! |
- if (inherits(modules, class)) {
+ landing_popup <- landing[[1L]] |
|
| 668 | +151 | ! |
- NULL+ modules <- drop_module(modules, "teal_module_landing") |
|
| 669 | +152 | ! |
- } else if (inherits(modules, "teal_module")) {
+ lifecycle::deprecate_soft( |
|
| 670 | +153 | ! |
- modules+ when = "0.15.3", |
|
| 671 | +154 | ! |
- } else if (inherits(modules, "teal_modules")) {
+ what = "landing_popup_module()", |
|
| 672 | +155 | ! |
- do.call(+ details = paste( |
|
| 673 | +156 | ! |
- "modules",+ "Pass `landing_popup_module` to the `landing_popup` argument of the `init` ", |
|
| 674 | +157 | ! |
- c(Filter(function(x) length(x) > 0L, lapply(modules$children, drop_module, class)), label = modules$label)+ "instead of wrapping it into `modules()` and passing to the `modules` argument" |
|
| 675 | +158 |
- )+ ) |
||
| 676 | +159 |
- }+ ) |
||
| 677 | -+ | |||
| 160 | +13x |
- }+ } else if (length(landing) > 1L) {
|
||
| 678 | -+ | |||
| 161 | +! |
-
+ stop("Only one `landing_popup_module` can be used.")
|
||
| 679 | +162 |
- ## read modules ----+ } |
||
| 680 | +163 | |||
| 681 | +164 |
- #' Does the object make use of the `arg`+ ## `filter` - set app_id attribute unless present (when restoring bookmark) |
||
| 682 | -+ | |||
| 165 | +13x |
- #'+ if (is.null(attr(filter, "app_id", exact = TRUE))) attr(filter, "app_id") <- create_app_id(data, modules) |
||
| 683 | +166 |
- #' @param modules (`teal_module` or `teal_modules`) object+ |
||
| 684 | +167 |
- #' @param arg (`character(1)`) names of the arguments to be checked against formals of `teal` modules.+ ## `filter` - convert teal.slice::teal_slices to teal::teal_slices |
||
| 685 | -+ | |||
| 168 | +13x |
- #' @return `logical` whether the object makes use of `arg`.+ filter <- as.teal_slices(as.list(filter)) |
||
| 686 | +169 |
- #' @rdname is_arg_used+ |
||
| 687 | +170 |
- #' @keywords internal+ # argument checking (interdependent) |
||
| 688 | +171 |
- is_arg_used <- function(modules, arg) {
+ ## `filter` - `modules` |
||
| 689 | -519x | +172 | +13x |
- checkmate::assert_string(arg)+ if (isTRUE(attr(filter, "module_specific"))) {
|
| 690 | -516x | +|||
| 173 | +! |
- if (inherits(modules, "teal_modules")) {
+ module_names <- unlist(c(module_labels(modules), "global_filters")) |
||
| 691 | -20x | +|||
| 174 | +! |
- any(unlist(lapply(modules$children, is_arg_used, arg)))+ failed_mod_names <- setdiff(names(attr(filter, "mapping")), module_names) |
||
| 692 | -496x | +|||
| 175 | +! |
- } else if (inherits(modules, "teal_module")) {
+ if (length(failed_mod_names)) {
|
||
| 693 | -32x | +|||
| 176 | +! |
- is_arg_used(modules$server, arg) || is_arg_used(modules$ui, arg)+ stop( |
||
| 694 | -464x | +|||
| 177 | +! |
- } else if (is.function(modules)) {
+ sprintf( |
||
| 695 | -462x | +|||
| 178 | +! |
- isTRUE(arg %in% names(formals(modules)))+ "Some module names in the mapping arguments don't match module labels.\n %s not in %s",+ |
+ ||
| 179 | +! | +
+ toString(failed_mod_names),+ |
+ ||
| 180 | +! | +
+ toString(unique(module_names)) |
||
| 696 | +181 |
- } else {
+ ) |
||
| 697 | -2x | +|||
| 182 | +
- stop("is_arg_used function not implemented for this object")
+ ) |
|||
| 698 | +183 |
- }+ } |
||
| 699 | +184 |
- }+ + |
+ ||
| 185 | +! | +
+ if (anyDuplicated(module_names)) {
|
||
| 700 | +186 |
-
+ # In teal we are able to set nested modules with duplicated label. |
||
| 701 | +187 |
-
+ # Because mapping argument bases on the relationship between module-label and filter-id, |
||
| 702 | +188 |
- #' Get module depth+ # it is possible that module-label in mapping might refer to multiple teal_module (identified by the same label)+ |
+ ||
| 189 | +! | +
+ stop(+ |
+ ||
| 190 | +! | +
+ sprintf(+ |
+ ||
| 191 | +! | +
+ "Module labels should be unique when teal_slices(mapping = TRUE). Duplicated labels:\n%s ",+ |
+ ||
| 192 | +! | +
+ toString(module_names[duplicated(module_names)]) |
||
| 703 | +193 |
- #'+ ) |
||
| 704 | +194 |
- #' Depth starts at 0, so a single `teal.module` has depth 0.+ ) |
||
| 705 | +195 | ++ |
+ }+ |
+ |
| 196 | ++ |
+ }+ |
+ ||
| 197 | ++ | + + | +||
| 198 |
- #' Nesting it increases overall depth by 1.+ ## `data` - `modules`+ |
+ |||
| 199 | +13x | +
+ if (inherits(data, "teal_data")) {
+ |
+ ||
| 200 | +12x | +
+ if (length(data) == 0) {
|
||
| 706 | -+ | |||
| 201 | +1x |
- #'+ stop("The environment of `data` is empty.")
|
||
| 707 | +202 |
- #' @inheritParams init+ } |
||
| 708 | +203 |
- #' @param depth optional integer determining current depth level+ |
||
| 709 | -+ | |||
| 204 | +11x |
- #'+ is_modules_ok <- check_modules_datanames(modules, names(data)) |
||
| 710 | -+ | |||
| 205 | +11x |
- #' @return Depth level for given module.+ if (!isTRUE(is_modules_ok) && length(unlist(extract_transformators(modules))) == 0) {
|
||
| 711 | -+ | |||
| 206 | +4x |
- #' @keywords internal+ warning(is_modules_ok, call. = FALSE) |
||
| 712 | +207 |
- modules_depth <- function(modules, depth = 0L) {
+ } |
||
| 713 | -12x | +|||
| 208 | +
- checkmate::assert_multi_class(modules, c("teal_module", "teal_modules"))
+
|
|||
| 714 | -12x | +209 | +11x |
- checkmate::assert_int(depth, lower = 0)+ is_filter_ok <- check_filter_datanames(filter, names(data)) |
| 715 | +210 | 11x |
- if (inherits(modules, "teal_modules")) {
+ if (!isTRUE(is_filter_ok)) {
|
|
| 716 | -4x | +211 | +1x |
- max(vapply(modules$children, modules_depth, integer(1), depth = depth + 1L))+ warning(is_filter_ok) |
| 717 | +212 |
- } else {
+ # we allow app to continue if applied filters are outside |
||
| 718 | -7x | +|||
| 213 | +
- depth+ # of possible data range |
|||
| 719 | +214 |
- }+ } |
||
| 720 | +215 |
- }+ } |
||
| 721 | +216 | |||
| 722 | -+ | |||
| 217 | +12x |
- #' Retrieve labels from `teal_modules`+ reporter <- teal.reporter::Reporter$new()$set_id(attr(filter, "app_id")) |
||
| 723 | -+ | |||
| 218 | +12x |
- #'+ if (is_arg_used(modules, "reporter") && length(extract_module(modules, "teal_module_previewer")) == 0) {
|
||
| 724 | -+ | |||
| 219 | +! |
- #' @param modules (`teal_modules`)+ modules <- append_module( |
||
| 725 | -+ | |||
| 220 | +! |
- #' @return A `list` containing the labels of the modules. If the modules are nested,+ modules, |
||
| 726 | -+ | |||
| 221 | +! |
- #' the function returns a nested `list` of labels.+ reporter_previewer_module(server_args = list(previewer_buttons = c("download", "reset")))
|
||
| 727 | +222 |
- #' @keywords internal+ ) |
||
| 728 | +223 |
- module_labels <- function(modules) {
+ } |
||
| 729 | -199x | +|||
| 224 | +
- if (inherits(modules, "teal_modules")) {
+
|
|||
| 730 | -87x | +225 | +12x |
- lapply(modules$children, module_labels)+ ns <- NS(id) |
| 731 | +226 |
- } else {
+ # Note: UI must be a function to support bookmarking. |
||
| 732 | -112x | +227 | +12x |
- modules$label+ res <- list( |
| 733 | -+ | |||
| 228 | +12x |
- }+ ui = function(request) {
|
||
| 734 | -+ | |||
| 229 | +! |
- }+ ui_teal( |
||
| 735 | -+ | |||
| 230 | +! |
-
+ id = ns("teal"),
|
||
| 736 | -+ | |||
| 231 | +! |
- #' Retrieve `teal_bookmarkable` attribute from `teal_modules`+ modules = modules, |
||
| 737 | -+ | |||
| 232 | +! |
- #'+ title = title, |
||
| 738 | -+ | |||
| 233 | +! |
- #' @param modules (`teal_modules` or `teal_module`) object+ header = header, |
||
| 739 | -+ | |||
| 234 | +! |
- #' @return named list of the same structure as `modules` with `TRUE` or `FALSE` values indicating+ footer = footer |
||
| 740 | +235 |
- #' whether the module is bookmarkable.+ ) |
||
| 741 | +236 |
- #' @keywords internal+ }, |
||
| 742 | -+ | |||
| 237 | +12x |
- modules_bookmarkable <- function(modules) {
+ server = function(input, output, session) {
|
||
| 743 | -199x | +|||
| 238 | +! |
- checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"))
+ if (!is.null(landing_popup)) {
|
||
| 744 | -199x | +|||
| 239 | +! |
- if (inherits(modules, "teal_modules")) {
+ do.call(landing_popup$server, c(list(id = "landing_module_shiny_id"), landing_popup$server_args)) |
||
| 745 | -87x | +|||
| 240 | +
- setNames(+ } |
|||
| 746 | -87x | +|||
| 241 | +! |
- lapply(modules$children, modules_bookmarkable),+ srv_teal(id = ns("teal"), data = data, modules = modules, filter = deep_copy_filter(filter))
|
||
| 747 | -87x | +|||
| 242 | +
- vapply(modules$children, `[[`, "label", FUN.VALUE = character(1))+ } |
|||
| 748 | +243 |
- )+ ) |
||
| 749 | +244 |
- } else {
+
|
||
| 750 | -112x | +245 | +12x |
- attr(modules, "teal_bookmarkable", exact = TRUE)+ logger::log_debug("init teal app has been initialized.")
|
| 751 | +246 |
- }+ + |
+ ||
| 247 | +12x | +
+ res |
||
| 752 | +248 |
}@@ -23970,63 +23165,63 @@ teal coverage - 60.11% |
| 1 |
- # FilteredData ------+ setOldClass("teal_module")
|
||
| 2 |
-
+ setOldClass("teal_modules")
|
||
| 3 |
- #' Drive a `teal` application+ |
||
| 4 |
- #'+ #' Create `teal_module` and `teal_modules` objects |
||
| 5 |
- #' Extension of the `shinytest2::AppDriver` class with methods for+ #' |
||
| 6 |
- #' driving a teal application for performing interactions for `shinytest2` tests.+ #' @description |
||
| 7 |
- #'+ #' `r lifecycle::badge("stable")`
|
||
| 8 |
- #' @keywords internal+ #' Create a nested tab structure to embed modules in a `teal` application. |
||
| 10 |
- TealAppDriver <- R6::R6Class( # nolint: object_name.+ #' @details |
||
| 11 |
- "TealAppDriver",+ #' `module()` creates an instance of a `teal_module` that can be placed in a `teal` application. |
||
| 12 |
- inherit = {
+ #' `modules()` shapes the structure of a the application by organizing `teal_module` within the navigation panel. |
||
| 13 |
- if (!requireNamespace("shinytest2", quietly = TRUE)) {
+ #' It wraps `teal_module` and `teal_modules` objects in a `teal_modules` object, |
||
| 14 |
- stop("Please install 'shinytest2' package to use this class.")
+ #' which results in a nested structure corresponding to the nested tabs in the final application. |
||
| 15 |
- }+ #' |
||
| 16 |
- if (!requireNamespace("rvest", quietly = TRUE)) {
+ #' Note that for `modules()` `label` comes after `...`, so it must be passed as a named argument, |
||
| 17 |
- stop("Please install 'rvest' package to use this class.")
+ #' otherwise it will be captured by `...`. |
||
| 18 |
- }+ #' |
||
| 19 |
- shinytest2::AppDriver+ #' The labels `"global_filters"` and `"Report previewer"` are reserved |
||
| 20 |
- },+ #' because they are used by the `mapping` argument of [teal_slices()] |
||
| 21 |
- # public methods ----+ #' and the report previewer module [reporter_previewer_module()], respectively. |
||
| 22 |
- public = list(+ #' |
||
| 23 |
- #' @description+ #' # Restricting datasets used by `teal_module`: |
||
| 24 |
- #' Initialize a `TealAppDriver` object for testing a `teal` application.+ #' 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 |
- #' @param data,modules,filter,title,header,footer,landing_popup arguments passed to `init`+ #' |
||
| 27 |
- #' @param timeout (`numeric`) Default number of milliseconds for any timeout or+ #' When `datanames` is set to `"all"`, all datasets in the data object are treated as relevant. |
||
| 28 |
- #' timeout_ parameter in the `TealAppDriver` class.+ #' However, this may include unnecessary datasets, such as: |
||
| 29 |
- #' Defaults to 20s.+ #' - Proxy variables for column modifications |
||
| 30 |
- #'+ #' - Temporary datasets used to create final versions |
||
| 31 |
- #' See [`shinytest2::AppDriver`] `new` method for more details on how to change it+ #' - Connection objects |
||
| 32 |
- #' via options or environment variables.+ #' |
||
| 33 |
- #' @param load_timeout (`numeric`) How long to wait for the app to load, in ms.+ #' To exclude irrelevant datasets, use the [set_datanames()] function to change `datanames` from |
||
| 34 |
- #' This includes the time to start R. Defaults to 100s.+ #' `"all"` to specific names. Trying to modify non-`"all"` values with [set_datanames()] will result |
||
| 35 |
- #'+ #' in a warning. Datasets with names starting with . are ignored globally unless explicitly listed |
||
| 36 |
- #' See [`shinytest2::AppDriver`] `new` method for more details on how to change it+ #' in `datanames`. |
||
| 37 |
- #' via options or environment variables+ #' |
||
| 38 |
- #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$new`+ #' # `datanames` with `transformators` |
||
| 39 |
- #'+ #' When transformators are specified, their `datanames` are added to the module’s `datanames`, which |
||
| 40 |
- #'+ #' changes the behavior as follows: |
||
| 41 |
- #' @return Object of class `TealAppDriver`+ #' - If `module(datanames)` is `NULL` and the `transformators` have defined `datanames`, the sidebar |
||
| 42 |
- initialize = function(data,+ #' will appear showing the `transformators`' datasets, instead of being hidden. |
||
| 43 |
- modules,+ #' - If `module(datanames)` is set to specific values and any `transformator` has `datanames = "all"`, |
||
| 44 |
- filter = teal_slices(),+ #' the module may receive extra datasets that could be unnecessary |
||
| 45 |
- title = build_app_title(),+ #' |
||
| 46 |
- header = tags$p(),+ #' @param label (`character(1)`) Label shown in the navigation item for the module or module group. |
||
| 47 |
- footer = tags$p(),+ #' For `modules()` defaults to `"root"`. See `Details`. |
||
| 48 |
- landing_popup = NULL,+ #' @param server (`function`) `shiny` module with following arguments: |
||
| 49 |
- timeout = rlang::missing_arg(),+ #' - `id` - `teal` will set proper `shiny` namespace for this module (see [shiny::moduleServer()]). |
||
| 50 |
- load_timeout = rlang::missing_arg(),+ #' - `input`, `output`, `session` - (optional; not recommended) When provided, then [shiny::callModule()] |
||
| 51 |
- ...) {
+ #' will be used to call a module. From `shiny` 1.5.0, the recommended way is to use |
||
| 52 | -! | +
- private$data <- data+ #' [shiny::moduleServer()] instead which doesn't require these arguments. |
|
| 53 | -! | +
- private$modules <- modules+ #' - `data` (optional) When provided, the module will be called with `teal_data` object (i.e. a list of |
|
| 54 | -! | +
- private$filter <- filter+ #' reactive (filtered) data specified in the `filters` argument) as the value of this argument. |
|
| 55 | -! | +
- app <- init(+ #' - `datasets` (optional) When provided, the module will be called with `FilteredData` object as the |
|
| 56 | -! | +
- data = data,+ #' value of this argument. (See [`teal.slice::FilteredData`]). |
|
| 57 | -! | +
- modules = modules,+ #' - `reporter` (optional) When provided, the module will be called with `Reporter` object as the value |
|
| 58 | -! | +
- filter = filter,+ #' of this argument. (See [`teal.reporter::Reporter`]). |
|
| 59 | -! | +
- title = title,+ #' - `filter_panel_api` (optional) When provided, the module will be called with `FilterPanelAPI` object |
|
| 60 | -! | +
- header = header,+ #' as the value of this argument. (See [`teal.slice::FilterPanelAPI`]). |
|
| 61 | -! | +
- footer = footer,+ #' - `...` (optional) When provided, `server_args` elements will be passed to the module named argument |
|
| 62 | -! | +
- landing_popup = landing_popup,+ #' 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 |
- # Default timeout is hardcoded to 4s in shinytest2:::resolve_timeout+ #' - `...` (optional) When provided, `ui_args` elements will be passed to the module named argument |
||
| 66 |
- # It must be set as parameter to the AppDriver+ #' or to the `...`. |
||
| 67 | -! | +
- suppressWarnings(+ #' @param filters (`character`) Deprecated. Use `datanames` instead. |
|
| 68 | -! | +
- super$initialize(+ #' @param datanames (`character`) Names of the datasets relevant to the item. |
|
| 69 | -! | +
- app_dir = shinyApp(app$ui, app$server),+ #' There are 2 reserved values that have specific behaviors: |
|
| 70 | -! | +
- name = "teal",+ #' - The keyword `"all"` includes all datasets available in the data passed to the teal application. |
|
| 71 | -! | +
- variant = shinytest2::platform_variant(),+ #' - `NULL` hides the sidebar panel completely. |
|
| 72 | -! | +
- timeout = rlang::maybe_missing(timeout, 20 * 1000),+ #' - If `transformators` are specified, their `datanames` are automatically added to this `datanames` |
|
| 73 | -! | +
- load_timeout = rlang::maybe_missing(load_timeout, 100 * 1000),+ #' argument. |
|
| 74 |
- ...+ #' @param server_args (named `list`) with additional arguments passed on to the server function. |
||
| 75 |
- )+ #' @param ui_args (named `list`) with additional arguments passed on to the UI function. |
||
| 76 |
- )+ #' @param x (`teal_module` or `teal_modules`) Object to format/print. |
||
| 77 |
-
+ #' @param transformators (`list` of `teal_transform_module`) that will be applied to transformator module's data input. |
||
| 78 |
- # Check for minimum version of Chrome that supports the tests+ #' |
||
| 79 |
- # - Element.checkVisibility was added on 105+ #' |
||
| 80 | -! | +
- chrome_version <- numeric_version(+ #' @param ... |
|
| 81 | -! | +
- gsub(+ #' - For `modules()`: (`teal_module` or `teal_modules`) Objects to wrap into a tab. |
|
| 82 | -! | +
- "[[:alnum:]_]+/", # Prefix that ends with forward slash+ #' - For `format()` and `print()`: Arguments passed to other methods. |
|
| 83 |
- "",+ #' |
||
| 84 | -! | +
- self$get_chromote_session()$Browser$getVersion()$product+ #' @return |
|
| 85 |
- ),+ #' `module()` returns an object of class `teal_module`. |
||
| 86 | -! | +
- strict = FALSE+ #' |
|
| 87 |
- )+ #' `modules()` returns a `teal_modules` object which contains following fields: |
||
| 88 |
-
+ #' - `label`: taken from the `label` argument. |
||
| 89 | -! | +
- required_version <- "121"+ #' - `children`: a list containing objects passed in `...`. List elements are named after |
|
| 90 |
-
+ #' their `label` attribute converted to a valid `shiny` id. |
||
| 91 | -! | +
- testthat::skip_if(+ #' |
|
| 92 | -! | +
- is.na(chrome_version),+ #' @name teal_modules |
|
| 93 | -! | +
- "Problem getting Chrome version, please contact the developers."+ #' @aliases teal_module |
|
| 94 |
- )+ #' |
||
| 95 | -! | +
- testthat::skip_if(+ #' @examples |
|
| 96 | -! | +
- chrome_version < required_version,+ #' library(shiny) |
|
| 97 | -! | +
- sprintf(+ #' |
|
| 98 | -! | +
- "Chrome version '%s' is not supported, please upgrade to '%s' or higher",+ #' module_1 <- module( |
|
| 99 | -! | +
- chrome_version,+ #' label = "a module", |
|
| 100 | -! | +
- required_version+ #' server = function(id, data) {
|
|
| 101 |
- )+ #' moduleServer( |
||
| 102 |
- )+ #' id, |
||
| 103 |
- # end od check+ #' module = function(input, output, session) {
|
||
| 104 |
-
+ #' output$data <- renderDataTable(data()[["iris"]]) |
||
| 105 | -! | +
- private$set_active_ns()+ #' } |
|
| 106 | -! | +
- self$wait_for_idle()+ #' ) |
|
| 107 |
- },+ #' }, |
||
| 108 |
- #' @description+ #' ui = function(id) {
|
||
| 109 |
- #' Append parent [`shinytest2::AppDriver`] `click` method with a call to `waif_for_idle()` method.+ #' ns <- NS(id) |
||
| 110 |
- #' @param ... arguments passed to parent [`shinytest2::AppDriver`] `click()` method.+ #' tagList(dataTableOutput(ns("data")))
|
||
| 111 |
- click = function(...) {
+ #' }, |
||
| 112 | -! | +
- super$click(...)+ #' datanames = "all" |
|
| 113 | -! | +
- private$wait_for_page_stability()+ #' ) |
|
| 114 |
- },+ #' |
||
| 115 |
- #' @description+ #' module_2 <- module( |
||
| 116 |
- #' Check if the app has shiny errors. This checks for global shiny errors.+ #' label = "another module", |
||
| 117 |
- #' Note that any shiny errors dependent on shiny server render will only be captured after the teal module tab+ #' server = function(id) {
|
||
| 118 |
- #' is visited because shiny will not trigger server computations when the tab is invisible.+ #' moduleServer( |
||
| 119 |
- #' So, navigate to the module tab you want to test before calling this function.+ #' id, |
||
| 120 |
- #' Although, this catches errors hidden in the other module tabs if they are already rendered.+ #' module = function(input, output, session) {
|
||
| 121 |
- expect_no_shiny_error = function() {
+ #' output$text <- renderText("Another Module")
|
||
| 122 | -! | +
- testthat::expect_null(+ #' } |
|
| 123 | -! | +
- self$get_html(".shiny-output-error:not(.shiny-output-error-validation)"),
+ #' ) |
|
| 124 | -! | +
- info = "Shiny error is observed"+ #' }, |
|
| 125 |
- )+ #' ui = function(id) {
|
||
| 126 |
- },+ #' ns <- NS(id) |
||
| 127 |
- #' @description+ #' tagList(textOutput(ns("text")))
|
||
| 128 |
- #' Check if the app has no validation errors. This checks for global shiny validation errors.+ #' }, |
||
| 129 |
- expect_no_validation_error = function() {
+ #' datanames = NULL |
||
| 130 | -! | +
- testthat::expect_null(+ #' ) |
|
| 131 | -! | +
- self$get_html(".shiny-output-error-validation"),
+ #' |
|
| 132 | -! | +
- info = "No validation error is observed"+ #' modules <- modules( |
|
| 133 |
- )+ #' label = "modules", |
||
| 134 |
- },+ #' modules( |
||
| 135 |
- #' @description+ #' label = "nested modules", |
||
| 136 |
- #' Check if the app has validation errors. This checks for global shiny validation errors.+ #' module_1 |
||
| 137 |
- expect_validation_error = function() {
+ #' ), |
||
| 138 | -! | +
- testthat::expect_false(+ #' module_2 |
|
| 139 | -! | +
- is.null(self$get_html(".shiny-output-error-validation")),
+ #' ) |
|
| 140 | -! | +
- info = "Validation error is not observed"+ #' |
|
| 141 |
- )+ #' app <- init( |
||
| 142 |
- },+ #' data = teal_data(iris = iris), |
||
| 143 |
- #' @description+ #' modules = modules |
||
| 144 |
- #' Set the input in the `teal` app.+ #' ) |
||
| 145 |
- #'+ #' |
||
| 146 |
- #' @param input_id (character) The shiny input id with it's complete name space.+ #' if (interactive()) {
|
||
| 147 |
- #' @param value The value to set the input to.+ #' shinyApp(app$ui, app$server) |
||
| 148 |
- #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$set_inputs`+ #' } |
||
| 149 |
- #'+ #' @rdname teal_modules |
||
| 150 |
- #' @return The `TealAppDriver` object invisibly.+ #' @export |
||
| 151 |
- set_input = function(input_id, value, ...) {
+ #' |
||
| 152 | -! | +
- do.call(+ module <- function(label = "module", |
|
| 153 | -! | +
- self$set_inputs,+ server = function(id, data, ...) moduleServer(id, function(input, output, session) NULL), |
|
| 154 | -! | +
- c(setNames(list(value), input_id), list(...))+ ui = function(id, ...) tags$p(paste0("This module has no UI (id: ", id, " )")),
|
|
| 155 |
- )+ filters, |
||
| 156 | -! | +
- invisible(self)+ datanames = "all", |
|
| 157 |
- },+ server_args = NULL, |
||
| 158 |
- #' @description+ ui_args = NULL, |
||
| 159 |
- #' Navigate the teal tabs in the `teal` app.+ transformators = list()) {
|
||
| 160 |
- #'+ # argument checking (independent) |
||
| 161 |
- #' @param tabs (character) Labels of tabs to navigate to. The order of the tabs is important,+ ## `label` |
||
| 162 | -+ | 220x |
- #' and it should start with the most parent level tab.+ checkmate::assert_string(label) |
| 163 | -+ | 217x |
- #' Note: In case the teal tab group has duplicate names, the first tab will be selected,+ if (label == "global_filters") {
|
| 164 | -+ | 1x |
- #' If you wish to select the second tab with the same name, use the suffix "_1".+ stop( |
| 165 | -+ | 1x |
- #' If you wish to select the third tab with the same name, use the suffix "_2" and so on.+ sprintf("module(label = \"%s\", ...\n ", label),
|
| 166 | -+ | 1x |
- #'+ "Label 'global_filters' is reserved in teal. Please change to something else.", |
| 167 | -+ | 1x |
- #' @return The `TealAppDriver` object invisibly.+ call. = FALSE |
| 168 |
- navigate_teal_tab = function(tabs) {
+ ) |
||
| 169 | -! | +
- checkmate::check_character(tabs, min.len = 1)+ } |
|
| 170 | -! | +216x |
- for (tab in tabs) {
+ if (label == "Report previewer") {
|
| 171 | ! |
- self$set_input(+ stop( |
|
| 172 | ! |
- "teal-teal_modules-active_tab",+ sprintf("module(label = \"%s\", ...\n ", label),
|
|
| 173 | ! |
- get_unique_labels(tab),+ "Label 'Report previewer' is reserved in teal. Please change to something else.", |
|
| 174 | ! |
- wait_ = FALSE+ call. = FALSE |
|
| 175 |
- )+ ) |
||
| 176 |
- }+ } |
||
| 177 | -! | +
- self$wait_for_idle()+ |
|
| 178 | -! | +
- private$set_active_ns()+ ## server |
|
| 179 | -! | +216x |
- invisible(self)+ checkmate::assert_function(server) |
| 180 | -+ | 216x |
- },+ server_formals <- names(formals(server)) |
| 181 | -+ | 216x |
- #' @description+ if (!( |
| 182 | -+ | 216x |
- #' Get the active shiny name space for different components of the teal app.+ "id" %in% server_formals || |
| 183 | -+ | 216x |
- #'+ all(c("input", "output", "session") %in% server_formals)
|
| 184 |
- #' @return (`list`) The list of active shiny name space of the teal components.+ )) {
|
||
| 185 | -+ | 2x |
- active_ns = function() {
+ stop( |
| 186 | -! | +2x |
- if (identical(private$ns$module, character(0))) {
+ "\nmodule() `server` argument requires a function with following arguments:", |
| 187 | -! | +2x |
- private$set_active_ns()+ "\n - id - `teal` will set proper `shiny` namespace for this module.", |
| 188 | -+ | 2x |
- }+ "\n - input, output, session (not recommended) - then `shiny::callModule` will be used to call a module.", |
| 189 | -! | +2x |
- private$ns+ "\n\nFollowing arguments can be used optionaly:", |
| 190 | -+ | 2x |
- },+ "\n - `data` - module will receive list of reactive (filtered) data specified in the `filters` argument", |
| 191 | -+ | 2x |
- #' @description+ "\n - `datasets` - module will receive `FilteredData`. See `help(teal.slice::FilteredData)`", |
| 192 | -+ | 2x |
- #' Get the active shiny name space for interacting with the module content.+ "\n - `reporter` - module will receive `Reporter`. See `help(teal.reporter::Reporter)`", |
| 193 | -+ | 2x |
- #'+ "\n - `filter_panel_api` - module will receive `FilterPanelAPI`. (See [teal.slice::FilterPanelAPI]).", |
| 194 | -+ | 2x |
- #' @return (`string`) The active shiny name space of the component.+ "\n - `...` server_args elements will be passed to the module named argument or to the `...`" |
| 195 |
- active_module_ns = function() {
+ ) |
||
| 196 | -! | +
- if (identical(private$ns$module, character(0))) {
+ } |
|
| 197 | -! | +
- private$set_active_ns()+ |
|
| 198 | -+ | 214x |
- }+ if ("datasets" %in% server_formals) {
|
| 199 | -! | +2x |
- private$ns$module+ warning( |
| 200 | -+ | 2x |
- },+ sprintf("Called from module(label = \"%s\", ...)\n ", label),
|
| 201 | -+ | 2x |
- #' @description+ "`datasets` argument in the server is deprecated and will be removed in the next release. ", |
| 202 | -+ | 2x |
- #' Get the active shiny name space bound with a custom `element` name.+ "Please use `data` instead.", |
| 203 | -+ | 2x |
- #'+ call. = FALSE |
| 204 |
- #' @param element `character(1)` custom element name.+ ) |
||
| 205 |
- #'+ } |
||
| 206 |
- #' @return (`string`) The active shiny name space of the component bound with the input `element`.+ |
||
| 207 |
- active_module_element = function(element) {
+ ## UI |
||
| 208 | -! | +214x |
- checkmate::assert_string(element)+ checkmate::assert_function(ui) |
| 209 | -! | +214x |
- sprintf("#%s-%s", self$active_module_ns(), element)
+ ui_formals <- names(formals(ui)) |
| 210 | -+ | 214x |
- },+ if (!"id" %in% ui_formals) {
|
| 211 | -+ | 1x |
- #' @description+ stop( |
| 212 | -+ | 1x |
- #' Get the text of the active shiny name space bound with a custom `element` name.+ "\nmodule() `ui` argument requires a function with following arguments:", |
| 213 | -+ | 1x |
- #'+ "\n - id - `teal` will set proper `shiny` namespace for this module.", |
| 214 | -+ | 1x |
- #' @param element `character(1)` the text of the custom element name.+ "\n\nFollowing arguments can be used optionally:", |
| 215 | -+ | 1x |
- #'+ "\n - `...` ui_args elements will be passed to the module argument of the same name or to the `...`" |
| 216 |
- #' @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 | -! | +213x |
- self$get_text(self$active_module_element(element))+ if (any(c("data", "datasets") %in% ui_formals)) {
|
| 220 | -+ | 2x |
- },+ stop( |
| 221 | -+ | 2x |
- #' @description+ sprintf("Called from module(label = \"%s\", ...)\n ", label),
|
| 222 | -+ | 2x |
- #' Get the active shiny name space for interacting with the filter panel.+ "UI with `data` or `datasets` argument is no longer accepted.\n ", |
| 223 | -+ | 2x |
- #'+ "If some UI inputs depend on data, please move the logic to your server instead.\n ", |
| 224 | -+ | 2x |
- #' @return (`string`) The active shiny name space of the component.+ "Possible solutions are renderUI() or updateXyzInput() functions." |
| 225 |
- active_filters_ns = function() {
+ ) |
||
| 226 | -! | +
- if (identical(private$ns$filter_panel, character(0))) {
+ } |
|
| 227 | -! | +
- private$set_active_ns()+ |
|
| 228 |
- }+ ## `filters` |
||
| 229 | -! | +211x |
- private$ns$filter_panel+ if (!missing(filters)) {
|
| 230 | -+ | ! |
- },+ datanames <- filters |
| 231 | -+ | ! |
- #' @description+ msg <- |
| 232 | -+ | ! |
- #' Get the active shiny name space for interacting with the data-summary panel.+ "The `filters` argument is deprecated and will be removed in the next release. Please use `datanames` instead." |
| 233 | -+ | ! |
- #'+ warning(msg) |
| 234 |
- #' @return (`string`) The active shiny name space of the data-summary component.+ } |
||
| 235 |
- active_data_summary_ns = function() {
+
|
||
| 236 | -! | +
- if (identical(private$ns$data_summary, character(0))) {
+ ## `datanames` (also including deprecated `filters`) |
|
| 237 | -! | +
- private$set_active_ns()+ # please note a race condition between datanames set when filters is not missing and data arg in server function |
|
| 238 | -+ | 211x |
- }+ if (!is.element("data", server_formals) && !is.null(datanames)) {
|
| 239 | -! | +12x |
- private$ns$data_summary+ message(sprintf("module \"%s\" server function takes no data so \"datanames\" will be ignored", label))
|
| 240 | -+ | 12x |
- },+ datanames <- NULL |
| 241 |
- #' @description+ } |
||
| 242 | -+ | 211x |
- #' Get the active shiny name space bound with a custom `element` name.+ checkmate::assert_character(datanames, min.len = 1, null.ok = TRUE, any.missing = FALSE) |
| 243 |
- #'+ |
||
| 244 |
- #' @param element `character(1)` custom element name.+ ## `server_args` |
||
| 245 | -+ | 210x |
- #'+ checkmate::assert_list(server_args, null.ok = TRUE, names = "named") |
| 246 | -+ | 208x |
- #' @return (`string`) The active shiny name space of the component bound with the input `element`.+ srv_extra_args <- setdiff(names(server_args), server_formals) |
| 247 | -+ | 208x |
- active_data_summary_element = function(element) {
+ if (length(srv_extra_args) > 0 && !"..." %in% server_formals) {
|
| 248 | -! | +1x |
- checkmate::assert_string(element)+ stop( |
| 249 | -! | +1x |
- sprintf("#%s-%s", self$active_data_summary_ns(), element)
+ "\nFollowing `server_args` elements have no equivalent in the formals of the server:\n", |
| 250 | -+ | 1x |
- },+ paste(paste(" -", srv_extra_args), collapse = "\n"),
|
| 251 | -+ | 1x |
- #' @description+ "\n\nUpdate the server arguments by including above or add `...`" |
| 252 |
- #' Get the input from the module in the `teal` app.+ ) |
||
| 253 |
- #' This function will only access inputs from the name space of the current active teal module.+ } |
||
| 254 |
- #'+ |
||
| 255 |
- #' @param input_id (character) The shiny input id to get the value from.+ ## `ui_args` |
||
| 256 | -+ | 207x |
- #'+ checkmate::assert_list(ui_args, null.ok = TRUE, names = "named") |
| 257 | -+ | 205x |
- #' @return The value of the shiny input.+ ui_extra_args <- setdiff(names(ui_args), ui_formals) |
| 258 | -+ | 205x |
- get_active_module_input = function(input_id) {
+ if (length(ui_extra_args) > 0 && !"..." %in% ui_formals) {
|
| 259 | -! | +1x |
- checkmate::check_string(input_id)+ stop( |
| 260 | -! | +1x |
- self$get_value(input = sprintf("%s-%s", self$active_module_ns(), input_id))
+ "\nFollowing `ui_args` elements have no equivalent in the formals of UI:\n", |
| 261 | -+ | 1x |
- },+ paste(paste(" -", ui_extra_args), collapse = "\n"),
|
| 262 | -+ | 1x |
- #' @description+ "\n\nUpdate the UI arguments by including above or add `...`" |
| 263 |
- #' Get the output from the module in the `teal` app.+ ) |
||
| 264 |
- #' This function will only access outputs from the name space of the current active teal module.+ } |
||
| 265 |
- #'+ |
||
| 266 |
- #' @param output_id (character) The shiny output id to get the value from.+ ## `transformators` |
||
| 267 | -+ | 204x |
- #'+ if (inherits(transformators, "teal_transform_module")) {
|
| 268 | -+ | 1x |
- #' @return The value of the shiny output.+ transformators <- list(transformators) |
| 269 |
- get_active_module_output = function(output_id) {
+ } |
||
| 270 | -! | +204x |
- checkmate::check_string(output_id)+ checkmate::assert_list(transformators, types = "teal_transform_module") |
| 271 | -! | +204x |
- self$get_value(output = sprintf("%s-%s", self$active_module_ns(), output_id))
+ transform_datanames <- unlist(lapply(transformators, attr, "datanames")) |
| 272 | -+ | 204x |
- },+ combined_datanames <- if (identical(datanames, "all")) {
|
| 273 | -+ | 151x |
- #' @description+ "all" |
| 274 |
- #' Get the output from the module's `teal.widgets::table_with_settings` or `DT::DTOutput` in the `teal` app.+ } else {
|
||
| 275 | -+ | 53x |
- #' This function will only access outputs from the name space of the current active teal module.+ union(datanames, transform_datanames) |
| 276 |
- #'+ } |
||
| 277 |
- #' @param table_id (`character(1)`) The id of the table in the active teal module's name space.+ |
||
| 278 | -+ | 204x |
- #' @param which (integer) If there is more than one table, which should be extracted.+ structure( |
| 279 | -+ | 204x |
- #' By default it will look for a table that is built using `teal.widgets::table_with_settings`.+ list( |
| 280 | -+ | 204x |
- #'+ label = label, |
| 281 | -+ | 204x |
- #' @return The data.frame with table contents.+ server = server, |
| 282 | -+ | 204x |
- get_active_module_table_output = function(table_id, which = 1) {
+ ui = ui, |
| 283 | -! | +204x |
- checkmate::check_number(which, lower = 1)+ datanames = combined_datanames, |
| 284 | -! | +204x |
- checkmate::check_string(table_id)+ server_args = server_args, |
| 285 | -! | +204x |
- table <- rvest::html_table(+ ui_args = ui_args, |
| 286 | -! | +204x |
- self$get_html_rvest(self$active_module_element(table_id)),+ transformators = transformators |
| 287 | -! | +
- fill = TRUE+ ), |
|
| 288 | -+ | 204x |
- )+ class = "teal_module" |
| 289 | -! | +
- if (length(table) == 0) {
+ ) |
|
| 290 | -! | +
- data.frame()+ } |
|
| 291 |
- } else {
+
|
||
| 292 | -! | +
- table[[which]]+ #' @rdname teal_modules |
|
| 293 |
- }+ #' @export |
||
| 294 |
- },+ #' |
||
| 295 |
- #' @description+ modules <- function(..., label = "root") {
|
||
| 296 | -+ | 144x |
- #' Get the output from the module's `teal.widgets::plot_with_settings` in the `teal` app.+ checkmate::assert_string(label) |
| 297 | -+ | 142x |
- #' This function will only access plots from the name space of the current active teal module.+ submodules <- list(...) |
| 298 | -+ | 142x |
- #'+ if (any(vapply(submodules, is.character, FUN.VALUE = logical(1)))) {
|
| 299 | -+ | 2x |
- #' @param plot_id (`character(1)`) The id of the plot in the active teal module's name space.+ stop( |
| 300 | -+ | 2x |
- #'+ "The only character argument to modules() must be 'label' and it must be named, ", |
| 301 | -+ | 2x |
- #' @return The `src` attribute as `character(1)` vector.+ "change modules('lab', ...) to modules(label = 'lab', ...)"
|
| 302 |
- get_active_module_plot_output = function(plot_id) {
+ ) |
||
| 303 | -! | +
- checkmate::check_string(plot_id)+ } |
|
| 304 | -! | +
- self$get_attr(+ |
|
| 305 | -! | +140x |
- self$active_module_element(sprintf("%s-plot_main > img", plot_id)),
+ checkmate::assert_list(submodules, min.len = 1, any.missing = FALSE, types = c("teal_module", "teal_modules"))
|
| 306 | -! | +
- "src"+ # name them so we can more easily access the children |
|
| 307 |
- )+ # beware however that the label of the submodules should not be changed as it must be kept synced |
||
| 308 | -+ | 137x |
- },+ labels <- vapply(submodules, function(submodule) submodule$label, character(1)) |
| 309 | -+ | 137x |
- #' @description+ names(submodules) <- get_unique_labels(labels) |
| 310 | -+ | 137x |
- #' Set the input in the module in the `teal` app.+ structure( |
| 311 | -+ | 137x |
- #' This function will only set inputs in the name space of the current active teal module.+ list( |
| 312 | -+ | 137x |
- #'+ label = label, |
| 313 | -+ | 137x |
- #' @param input_id (character) The shiny input id to get the value from.+ children = submodules |
| 314 |
- #' @param value The value to set the input to.+ ), |
||
| 315 | -+ | 137x |
- #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$set_inputs`+ class = "teal_modules" |
| 316 |
- #'+ ) |
||
| 317 |
- #' @return The `TealAppDriver` object invisibly.+ } |
||
| 318 |
- set_active_module_input = function(input_id, value, ...) {
+
|
||
| 319 | -! | +
- checkmate::check_string(input_id)+ # printing methods ---- |
|
| 320 | -! | +
- checkmate::check_string(value)+ |
|
| 321 | -! | +
- self$set_input(+ #' @rdname teal_modules |
|
| 322 | -! | +
- sprintf("%s-%s", self$active_module_ns(), input_id),
+ #' @param is_last (`logical(1)`) Whether this is the last item in its parent's children list. |
|
| 323 | -! | +
- value,+ #' Affects the tree branch character used (L- vs |-) |
|
| 324 |
- ...+ #' @param parent_prefix (`character(1)`) The prefix inherited from parent nodes, |
||
| 325 |
- )+ #' used to maintain the tree structure in nested levels |
||
| 326 | -! | +
- dots <- rlang::list2(...)+ #' @param is_root (`logical(1)`) Whether this is the root node of the tree. Only used in |
|
| 327 | -! | +
- if (!isFALSE(dots[["wait"]])) self$wait_for_idle() # Default behavior is to wait+ #' format.teal_modules(). Determines whether to show "TEAL ROOT" header |
|
| 328 | -! | +
- invisible(self)+ #' @param what (`character`) Specifies which metadata to display. |
|
| 329 |
- },+ #' Possible values: "datasets", "properties", "ui_args", "server_args", "transformators" |
||
| 330 |
- #' @description+ #' @examples |
||
| 331 |
- #' Get the active datasets that can be accessed via the filter panel of the current active teal module.+ #' mod <- module( |
||
| 332 |
- get_active_filter_vars = function() {
+ #' label = "My Custom Module", |
||
| 333 | -! | +
- displayed_datasets_index <- self$is_visible(+ #' server = function(id, data, ...) {},
|
|
| 334 | -! | +
- sprintf("#%s-filters-filter_active_vars_contents > span", self$active_filters_ns())
+ #' ui = function(id, ...) {},
|
|
| 335 |
- )+ #' datanames = c("ADSL", "ADTTE"),
|
||
| 336 |
-
+ #' transformators = list(), |
||
| 337 | -! | +
- available_datasets <- self$get_text(+ #' ui_args = list(a = 1, b = "b"), |
|
| 338 | -! | +
- sprintf(+ #' server_args = list(x = 5, y = list(p = 1)) |
|
| 339 | -! | +
- "#%s-filters-filter_active_vars_contents .filter_panel_dataname",+ #' ) |
|
| 340 | -! | +
- self$active_filters_ns()+ #' cat(format(mod)) |
|
| 341 |
- )+ #' @export |
||
| 342 |
- )+ format.teal_module <- function( |
||
| 343 |
-
+ x, is_last = FALSE, parent_prefix = "", |
||
| 344 | -! | +
- available_datasets[displayed_datasets_index]+ what = c("datasets", "properties", "ui_args", "server_args", "transformators"), ...) {
|
|
| 345 | -+ | 3x |
- },+ empty_text <- "" |
| 346 | -+ | 3x |
- #' @description+ branch <- if (is_last) "L-" else "|-" |
| 347 | -+ | 3x |
- #' Get the active data summary table+ current_prefix <- paste0(parent_prefix, branch, " ") |
| 348 | -+ | 3x |
- #' @return `data.frame`+ content_prefix <- paste0(parent_prefix, if (is_last) " " else "| ") |
| 349 |
- get_active_data_summary_table = function() {
+
|
||
| 350 | -! | +3x |
- summary_table <- rvest::html_table(+ format_list <- function(lst, empty = empty_text, label_width = 0) {
|
| 351 | -! | +6x |
- self$get_html_rvest(self$active_data_summary_element("table")),
+ if (is.null(lst) || length(lst) == 0) {
|
| 352 | -! | +6x |
- fill = TRUE+ empty |
| 353 | -! | +
- )[[1]]+ } else {
|
|
| 354 | -+ | ! |
-
+ colon_space <- paste(rep(" ", label_width), collapse = "")
|
| 355 | -! | +
- col_names <- unlist(summary_table[1, ], use.names = FALSE)+ |
|
| 356 | ! |
- summary_table <- summary_table[-1, ]+ first_item <- sprintf("%s (%s)", names(lst)[1], crayon::silver(class(lst[[1]])[1]))
|
|
| 357 | ! |
- colnames(summary_table) <- col_names+ rest_items <- if (length(lst) > 1) {
|
|
| 358 | ! |
- if (nrow(summary_table) > 0) {
+ paste( |
|
| 359 | ! |
- summary_table+ vapply( |
|
| 360 | -+ | ! |
- } else {
+ names(lst)[-1], |
| 361 | ! |
- NULL+ function(name) {
|
|
| 362 | -+ | ! |
- }+ sprintf( |
| 363 | -+ | ! |
- },+ "%s%s (%s)", |
| 364 | -+ | ! |
- #' @description+ paste0(content_prefix, "| ", colon_space), |
| 365 | -+ | ! |
- #' Test if `DOM` elements are visible on the page with a JavaScript call.+ name, |
| 366 | -+ | ! |
- #' @param selector (`character(1)`) `CSS` selector to check visibility.+ crayon::silver(class(lst[[name]])[1]) |
| 367 |
- #' A `CSS` id will return only one element if the UI is well formed.+ ) |
||
| 368 |
- #' @param content_visibility_auto,opacity_property,visibility_property (`logical(1)`) See more information+ }, |
||
| 369 | -+ | ! |
- #' on <https://developer.mozilla.org/en-US/docs/Web/API/Element/checkVisibility>.+ character(1) |
| 370 |
- #'+ ), |
||
| 371 | -+ | ! |
- #' @return Logical vector with all occurrences of the selector.+ collapse = "\n" |
| 372 |
- is_visible = function(selector,+ ) |
||
| 373 |
- content_visibility_auto = FALSE,+ } |
||
| 374 | -+ | ! |
- opacity_property = FALSE,+ if (length(lst) > 1) paste0(first_item, "\n", rest_items) else first_item |
| 375 |
- visibility_property = FALSE) {
+ } |
||
| 376 | -! | +
- checkmate::assert_string(selector)+ } |
|
| 377 | -! | +
- checkmate::assert_flag(content_visibility_auto)+ |
|
| 378 | -! | +3x |
- checkmate::assert_flag(opacity_property)+ bookmarkable <- isTRUE(attr(x, "teal_bookmarkable")) |
| 379 | -! | +3x |
- checkmate::assert_flag(visibility_property)+ reportable <- "reporter" %in% names(formals(x$server)) |
| 381 | -! | +3x |
- private$wait_for_page_stability()+ transformators <- if (length(x$transformators) > 0) {
|
| 382 | -+ | ! |
-
+ paste(sapply(x$transformators, function(t) attr(t, "label")), collapse = ", ") |
| 383 | -! | +
- testthat::skip_if_not(+ } else {
|
|
| 384 | -! | +3x |
- self$get_js("typeof Element.prototype.checkVisibility === 'function'"),
+ empty_text |
| 385 | -! | +
- "Element.prototype.checkVisibility is not supported in the current browser."+ } |
|
| 386 |
- )+ |
||
| 387 | -+ | 3x |
-
+ output <- pasten(current_prefix, crayon::bgWhite(x$label)) |
| 388 | -! | +
- unlist(+ |
|
| 389 | -! | +3x |
- self$get_js(+ if ("datasets" %in% what) {
|
| 390 | -! | +3x |
- sprintf(+ output <- paste0( |
| 391 | -! | +3x |
- "Array.from(document.querySelectorAll('%s')).map(el => el.checkVisibility({%s, %s, %s}))",
+ output, |
| 392 | -! | +3x |
- selector,+ content_prefix, "|- ", crayon::yellow("Datasets : "), paste(x$datanames, collapse = ", "), "\n"
|
| 393 |
- # Extra parameters+ ) |
||
| 394 | -! | +
- sprintf("contentVisibilityAuto: %s", tolower(content_visibility_auto)),
+ } |
|
| 395 | -! | +3x |
- sprintf("opacityProperty: %s", tolower(opacity_property)),
+ if ("properties" %in% what) {
|
| 396 | -! | +3x |
- sprintf("visibilityProperty: %s", tolower(visibility_property))
+ output <- paste0( |
| 397 | -+ | 3x |
- )+ output, |
| 398 | -+ | 3x |
- )+ content_prefix, "|- ", crayon::blue("Properties:"), "\n",
|
| 399 | -+ | 3x |
- )+ content_prefix, "| |- ", crayon::cyan("Bookmarkable : "), bookmarkable, "\n",
|
| 400 | -+ | 3x |
- },+ content_prefix, "| L- ", crayon::cyan("Reportable : "), reportable, "\n"
|
| 401 |
- #' @description+ ) |
||
| 402 |
- #' Get the active filter variables from a dataset in the `teal` app.+ } |
||
| 403 | -+ | 3x |
- #'+ if ("ui_args" %in% what) {
|
| 404 | -+ | 3x |
- #' @param dataset_name (character) The name of the dataset to get the filter variables from.+ ui_args_formatted <- format_list(x$ui_args, label_width = 19) |
| 405 | -+ | 3x |
- #' If `NULL`, the filter variables for all the datasets will be returned in a list.+ output <- paste0( |
| 406 | -+ | 3x |
- get_active_data_filters = function(dataset_name = NULL) {
+ output, |
| 407 | -! | +3x |
- checkmate::check_string(dataset_name, null.ok = TRUE)+ content_prefix, "|- ", crayon::green("UI Arguments : "), ui_args_formatted, "\n"
|
| 408 | -! | +
- datasets <- self$get_active_filter_vars()+ ) |
|
| 409 | -! | +
- checkmate::assert_subset(dataset_name, datasets)+ } |
|
| 410 | -! | +3x |
- active_filters <- lapply(+ if ("server_args" %in% what) {
|
| 411 | -! | +3x |
- datasets,+ server_args_formatted <- format_list(x$server_args, label_width = 19) |
| 412 | -! | +3x |
- function(x) {
+ output <- paste0( |
| 413 | -! | +3x |
- var_names <- gsub(+ output, |
| 414 | -! | +3x |
- pattern = "\\s",+ content_prefix, "|- ", crayon::green("Server Arguments : "), server_args_formatted, "\n"
|
| 415 | -! | +
- replacement = "",+ ) |
|
| 416 | -! | +
- self$get_text(+ } |
|
| 417 | -! | +3x |
- sprintf(+ if ("transformators" %in% what) {
|
| 418 | -! | +3x |
- "#%s-filters-%s .filter-card-varname",+ output <- paste0( |
| 419 | -! | +3x |
- self$active_filters_ns(),+ output, |
| 420 | -! | +3x |
- x+ content_prefix, "L- ", crayon::magenta("Transformators : "), transformators, "\n"
|
| 421 |
- )+ ) |
||
| 422 |
- )+ } |
||
| 423 |
- )+ |
||
| 424 | -! | +3x |
- structure(+ output |
| 425 | -! | +
- lapply(var_names, private$get_active_filter_selection, dataset_name = x),+ } |
|
| 426 | -! | +
- names = var_names+ |
|
| 427 |
- )+ #' @rdname teal_modules |
||
| 428 |
- }+ #' @examples |
||
| 429 |
- )+ #' custom_module <- function( |
||
| 430 | -! | +
- names(active_filters) <- datasets+ #' label = "label", ui_args = NULL, server_args = NULL, |
|
| 431 | -! | +
- if (is.null(dataset_name)) {
+ #' datanames = "all", transformators = list(), bk = FALSE) {
|
|
| 432 | -! | +
- return(active_filters)+ #' ans <- module( |
|
| 433 |
- }+ #' label, |
||
| 434 | -! | +
- active_filters[[dataset_name]]+ #' server = function(id, data, ...) {},
|
|
| 435 |
- },+ #' ui = function(id, ...) {
|
||
| 436 |
- #' @description+ #' }, |
||
| 437 |
- #' Add a new variable from the dataset to be filtered.+ #' datanames = datanames, |
||
| 438 |
- #'+ #' transformators = transformators, |
||
| 439 |
- #' @param dataset_name (character) The name of the dataset to add the filter variable to.+ #' ui_args = ui_args, |
||
| 440 |
- #' @param var_name (character) The name of the variable to add to the filter panel.+ #' server_args = server_args |
||
| 441 |
- #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$set_inputs`+ #' ) |
||
| 442 |
- #'+ #' attr(ans, "teal_bookmarkable") <- bk |
||
| 443 |
- #' @return The `TealAppDriver` object invisibly.+ #' ans |
||
| 444 |
- add_filter_var = function(dataset_name, var_name, ...) {
+ #' } |
||
| 445 | -! | +
- checkmate::check_string(dataset_name)+ #' |
|
| 446 | -! | +
- checkmate::check_string(var_name)+ #' dummy_transformator <- teal_transform_module( |
|
| 447 | -! | +
- private$set_active_ns()+ #' label = "Dummy Transform", |
|
| 448 | -! | +
- self$click(+ #' ui = function(id) div("(does nothing)"),
|
|
| 449 | -! | +
- selector = sprintf(+ #' server = function(id, data) {
|
|
| 450 | -! | +
- "#%s-filters-%s-add_filter_icon",+ #' moduleServer(id, function(input, output, session) data) |
|
| 451 | -! | +
- private$ns$filter_panel,+ #' } |
|
| 452 | -! | +
- dataset_name+ #' ) |
|
| 453 |
- )+ #' |
||
| 454 |
- )+ #' plot_transformator <- teal_transform_module( |
||
| 455 | -! | +
- self$set_input(+ #' label = "Plot Settings", |
|
| 456 | -! | +
- sprintf(+ #' ui = function(id) div("(does nothing)"),
|
|
| 457 | -! | +
- "%s-filters-%s-%s-filter-var_to_add",+ #' server = function(id, data) {
|
|
| 458 | -! | +
- private$ns$filter_panel,+ #' moduleServer(id, function(input, output, session) data) |
|
| 459 | -! | +
- dataset_name,+ #' } |
|
| 460 | -! | +
- dataset_name+ #' ) |
|
| 461 |
- ),+ #' |
||
| 462 | -! | +
- var_name,+ #' complete_modules <- modules( |
|
| 463 |
- ...+ #' custom_module( |
||
| 464 |
- )+ #' label = "Data Overview", |
||
| 465 | -! | +
- invisible(self)+ #' datanames = c("ADSL", "ADAE", "ADVS"),
|
|
| 466 |
- },+ #' ui_args = list( |
||
| 467 |
- #' @description+ #' view_type = "table", |
||
| 468 |
- #' Remove an active filter variable of a dataset from the active filter variables panel.+ #' page_size = 10, |
||
| 469 |
- #'+ #' filters = c("ARM", "SEX", "RACE")
|
||
| 470 |
- #' @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.+ #' server_args = list( |
||
| 472 |
- #' @param var_name (character) The name of the variable to remove from the filter panel.+ #' cache = TRUE, |
||
| 473 |
- #' If `NULL`, all the filter variables of the dataset will be removed.+ #' debounce = 1000 |
||
| 474 |
- #'+ #' ), |
||
| 475 |
- #' @return The `TealAppDriver` object invisibly.+ #' transformators = list(dummy_transformator), |
||
| 476 |
- remove_filter_var = function(dataset_name = NULL, var_name = NULL) {
+ #' bk = TRUE |
||
| 477 | -! | +
- checkmate::check_string(dataset_name, null.ok = TRUE)+ #' ), |
|
| 478 | -! | +
- checkmate::check_string(var_name, null.ok = TRUE)+ #' modules( |
|
| 479 | -! | +
- if (is.null(dataset_name)) {
+ #' label = "Nested 1", |
|
| 480 | -! | +
- remove_selector <- sprintf(+ #' custom_module( |
|
| 481 | -! | +
- "#%s-active-remove_all_filters",+ #' label = "Interactive Plots", |
|
| 482 | -! | +
- self$active_filters_ns()+ #' datanames = c("ADSL", "ADVS"),
|
|
| 483 |
- )+ #' ui_args = list( |
||
| 484 | -! | +
- } else if (is.null(var_name)) {
+ #' plot_type = c("scatter", "box", "line"),
|
|
| 485 | -! | +
- remove_selector <- sprintf(+ #' height = 600, |
|
| 486 | -! | +
- "#%s-active-%s-remove_filters",+ #' width = 800, |
|
| 487 | -! | +
- self$active_filters_ns(),+ #' color_scheme = "viridis" |
|
| 488 | -! | +
- dataset_name+ #' ), |
|
| 489 |
- )+ #' server_args = list( |
||
| 490 |
- } else {
+ #' render_type = "svg", |
||
| 491 | -! | +
- remove_selector <- sprintf(+ #' cache_plots = TRUE |
|
| 492 | -! | +
- "#%s-active-%s-filter-%s_%s-remove",+ #' ), |
|
| 493 | -! | +
- self$active_filters_ns(),+ #' transformators = list(dummy_transformator, plot_transformator), |
|
| 494 | -! | +
- dataset_name,+ #' bk = TRUE |
|
| 495 | -! | +
- dataset_name,+ #' ), |
|
| 496 | -! | +
- var_name+ #' modules( |
|
| 497 |
- )+ #' label = "Nested 2", |
||
| 498 |
- }+ #' custom_module( |
||
| 499 | -! | +
- self$click(+ #' label = "Summary Statistics", |
|
| 500 | -! | +
- selector = remove_selector+ #' datanames = "ADSL", |
|
| 501 |
- )+ #' ui_args = list( |
||
| 502 | -! | +
- invisible(self)+ #' stats = c("mean", "median", "sd", "range"),
|
|
| 503 |
- },+ #' grouping = c("ARM", "SEX")
|
||
| 504 |
- #' @description+ #' ) |
||
| 505 |
- #' Set the active filter values for a variable of a dataset in the active filter variable panel.+ #' ), |
||
| 506 |
- #'+ #' modules( |
||
| 507 |
- #' @param dataset_name (character) The name of the dataset to set the filter value for.+ #' label = "Labeled nested modules", |
||
| 508 |
- #' @param var_name (character) The name of the variable to set the filter value for.+ #' custom_module( |
||
| 509 |
- #' @param input The value to set the filter to.+ #' label = "Subgroup Analysis", |
||
| 510 |
- #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$set_inputs`+ #' datanames = c("ADSL", "ADAE"),
|
||
| 511 |
- #'+ #' ui_args = list( |
||
| 512 |
- #' @return The `TealAppDriver` object invisibly.+ #' subgroups = c("AGE", "SEX", "RACE"),
|
||
| 513 |
- set_active_filter_selection = function(dataset_name,+ #' analysis_type = "stratified" |
||
| 514 |
- var_name,+ #' ), |
||
| 515 |
- input,+ #' bk = TRUE |
||
| 516 |
- ...) {
+ #' ) |
||
| 517 | -! | +
- checkmate::check_string(dataset_name)+ #' ), |
|
| 518 | -! | +
- checkmate::check_string(var_name)+ #' modules(custom_module(label = "Subgroup Analysis in non-labled modules")) |
|
| 519 | -! | +
- checkmate::check_string(input)+ #' ) |
|
| 520 |
-
+ #' ), |
||
| 521 | -! | +
- input_id_prefix <- sprintf(+ #' custom_module("Non-nested module")
|
|
| 522 | -! | +
- "%s-filters-%s-filter-%s_%s-inputs",+ #' ) |
|
| 523 | -! | +
- self$active_filters_ns(),+ #' |
|
| 524 | -! | +
- dataset_name,+ #' cat(format(complete_modules)) |
|
| 525 | -! | +
- dataset_name,+ #' cat(format(complete_modules, what = c("ui_args", "server_args", "transformators")))
|
|
| 526 | -! | +
- var_name+ #' @export |
|
| 527 |
- )+ format.teal_modules <- function(x, is_root = TRUE, is_last = FALSE, parent_prefix = "", ...) {
|
||
| 528 | -+ | 1x |
-
+ if (is_root) {
|
| 529 | -+ | 1x |
- # Find the type of filter (based on filter panel)+ header <- pasten(crayon::bold("TEAL ROOT"))
|
| 530 | -! | +1x |
- supported_suffix <- c("selection", "selection_manual")
+ new_parent_prefix <- " " #' Initial indent for root level |
| 531 | -! | +
- slices_suffix <- supported_suffix[+ } else {
|
|
| 532 | ! |
- match(+ if (!is.null(x$label)) {
|
|
| 533 | ! |
- TRUE,+ branch <- if (is_last) "L-" else "|-" |
|
| 534 | ! |
- vapply(+ header <- pasten(parent_prefix, branch, " ", crayon::bold(x$label)) |
|
| 535 | ! |
- supported_suffix,+ new_parent_prefix <- paste0(parent_prefix, if (is_last) " " else "| ") |
|
| 536 | -! | +
- function(suffix) {
+ } else {
|
|
| 537 | ! |
- !is.null(self$get_html(sprintf("#%s-%s", input_id_prefix, suffix)))
+ header <- "" |
|
| 538 | -+ | ! |
- },+ new_parent_prefix <- parent_prefix |
| 539 | -! | +
- logical(1)+ } |
|
| 540 |
- )+ } |
||
| 541 |
- )+ |
||
| 542 | -+ | 1x |
- ]+ if (length(x$children) > 0) {
|
| 543 | -+ | 1x |
-
+ children_output <- character(0) |
| 544 | -+ | 1x |
- # Generate correct namespace+ n_children <- length(x$children) |
| 545 | -! | +
- slices_input_id <- sprintf(+ |
|
| 546 | -! | +1x |
- "%s-filters-%s-filter-%s_%s-inputs-%s",+ for (i in seq_along(x$children)) {
|
| 547 | -! | +3x |
- self$active_filters_ns(),+ child <- x$children[[i]] |
| 548 | -! | +3x |
- dataset_name,+ is_last_child <- (i == n_children) |
| 549 | -! | +
- dataset_name,+ |
|
| 550 | -! | +3x |
- var_name,+ if (inherits(child, "teal_modules")) {
|
| 551 | ! |
- slices_suffix+ children_output <- c( |
|
| 552 | -+ | ! |
- )+ children_output, |
| 553 | -+ | ! |
-
+ format(child, |
| 554 | ! |
- if (identical(slices_suffix, "selection_manual")) {
+ is_root = FALSE, |
|
| 555 | ! |
- checkmate::assert_numeric(input, len = 2)+ is_last = is_last_child, |
|
| 556 | -+ | ! |
-
+ parent_prefix = new_parent_prefix, |
| 557 | -! | +
- dots <- rlang::list2(...)+ ... |
|
| 558 | -! | +
- checkmate::assert_choice(dots$priority_, formals(self$set_inputs)[["priority_"]], null.ok = TRUE)+ ) |
|
| 559 | -! | +
- checkmate::assert_flag(dots$wait_, null.ok = TRUE)+ ) |
|
| 560 |
-
+ } else {
|
||
| 561 | -! | +3x |
- self$run_js(+ children_output <- c( |
| 562 | -! | +3x |
- sprintf(+ children_output, |
| 563 | -! | +3x |
- "Shiny.setInputValue('%s:sw.numericRange', [%f, %f], {priority: '%s'})",
+ format(child, |
| 564 | -! | +3x |
- slices_input_id,+ is_last = is_last_child, |
| 565 | -! | +3x |
- input[[1]],+ parent_prefix = new_parent_prefix, |
| 566 | -! | +
- input[[2]],+ ... |
|
| 567 | -! | +
- priority_ = ifelse(is.null(dots$priority_), "input", dots$priority_)+ ) |
|
| 568 |
- )+ ) |
||
| 569 |
- )+ } |
||
| 570 |
-
+ } |
||
| 571 | -! | +
- if (isTRUE(dots$wait_) || is.null(dots$wait_)) {
+
|
|
| 572 | -! | +1x |
- self$wait_for_idle(+ paste0(header, paste(children_output, collapse = "")) |
| 573 | -! | +
- timeout = if (is.null(dots$timeout_)) rlang::missing_arg() else dots$timeout_+ } else {
|
|
| 574 | -+ | ! |
- )+ header |
| 575 |
- }+ } |
||
| 576 | -! | +
- } else if (identical(slices_suffix, "selection")) {
+ } |
|
| 577 | -! | +
- self$set_input(+ |
|
| 578 | -! | +
- slices_input_id,+ #' @rdname teal_modules |
|
| 579 | -! | +
- input,+ #' @export |
|
| 580 |
- ...+ print.teal_module <- function(x, ...) {
|
||
| 581 | -+ | ! |
- )+ cat(format(x, ...)) |
| 582 | -+ | ! |
- } else {
+ invisible(x) |
| 583 | -! | +
- stop("Filter selection set not supported for this slice.")
+ } |
|
| 584 |
- }+ |
||
| 585 |
-
+ #' @rdname teal_modules |
||
| 586 | -! | +
- invisible(self)+ #' @export |
|
| 587 |
- },+ print.teal_modules <- function(x, ...) {
|
||
| 588 | -+ | ! |
- #' @description+ cat(format(x, ...)) |
| 589 | -+ | ! |
- #' Extract `html` attribute (found by a `selector`).+ invisible(x) |
| 590 |
- #'+ } |
||
| 591 |
- #' @param selector (`character(1)`) specifying the selector to be used to get the content of a specific node.+ |
||
| 592 |
- #' @param attribute (`character(1)`) name of an attribute to retrieve from a node specified by `selector`.+ #' @param modules (`teal_module` or `teal_modules`) |
||
| 593 |
- #'+ #' @rdname teal_modules |
||
| 594 |
- #' @return The `character` vector.+ #' @examples |
||
| 595 |
- get_attr = function(selector, attribute) {
+ #' # change the module's datanames |
||
| 596 | -! | +
- rvest::html_attr(+ #' set_datanames(module(datanames = "all"), "a") |
|
| 597 | -! | +
- rvest::html_nodes(self$get_html_rvest("html"), selector),
+ #' |
|
| 598 | -! | +
- attribute+ #' # change modules' datanames |
|
| 599 |
- )+ #' set_datanames( |
||
| 600 |
- },+ #' modules( |
||
| 601 |
- #' @description+ #' module(datanames = "all"), |
||
| 602 |
- #' Wrapper around `get_html` that passes the output directly to `rvest::read_html`.+ #' module(datanames = "a") |
||
| 603 |
- #'+ #' ), |
||
| 604 |
- #' @param selector `(character(1))` passed to `get_html`.+ #' "b" |
||
| 605 |
- #'+ #' ) |
||
| 606 |
- #' @return An XML document.+ #' @export |
||
| 607 |
- get_html_rvest = function(selector) {
+ set_datanames <- function(modules, datanames) {
|
||
| 608 | ! |
- rvest::read_html(self$get_html(selector))+ checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"))
|
|
| 609 | -+ | ! |
- },+ if (inherits(modules, "teal_modules")) {
|
| 610 | -+ | ! |
- #' Wrapper around `get_url()` method that opens the app in the browser.+ modules$children <- lapply(modules$children, set_datanames, datanames) |
| 611 |
- #'+ } else {
|
||
| 612 | -+ | ! |
- #' @return Nothing. Opens the underlying teal app in the browser.+ if (identical(modules$datanames, "all")) {
|
| 613 | -+ | ! |
- open_url = function() {
+ modules$datanames <- datanames |
| 614 | -! | +
- browseURL(self$get_url())+ } else {
|
|
| 615 | -+ | ! |
- },+ warning( |
| 616 | -+ | ! |
- #' @description+ "Not possible to modify datanames of the module ", modules$label, |
| 617 | -+ | ! |
- #' Waits until a specified input, output, or export value.+ ". set_datanames() can only change datanames if it was set to \"all\".", |
| 618 | -+ | ! |
- #' This function serves as a wrapper around the `wait_for_value` method,+ call. = FALSE |
| 619 |
- #' providing a more flexible interface for waiting on different types of values within the active module namespace.+ ) |
||
| 620 |
- #' @param input,output,export A name of an input, output, or export value.+ } |
||
| 621 |
- #' Only one of these parameters may be used.+ } |
||
| 622 | -+ | ! |
- #' @param ... Must be empty. Allows for parameter expansion.+ modules |
| 623 |
- #' Parameter with additional value to passed in `wait_for_value`.+ } |
||
| 624 |
- wait_for_active_module_value = function(input = rlang::missing_arg(),+ |
||
| 625 |
- output = rlang::missing_arg(),+ # utilities ---- |
||
| 626 |
- export = rlang::missing_arg(),+ ## subset or modify modules ---- |
||
| 627 |
- ...) {
+
|
||
| 628 | -! | +
- ns <- shiny::NS(self$active_module_ns())+ #' Append a `teal_module` to `children` of a `teal_modules` object |
|
| 629 |
-
+ #' @keywords internal |
||
| 630 | -! | +
- if (!rlang::is_missing(input) && checkmate::test_string(input, min.chars = 1)) input <- ns(input)+ #' @param modules (`teal_modules`) |
|
| 631 | -! | +
- if (!rlang::is_missing(output) && checkmate::test_string(output, min.chars = 1)) output <- ns(output)+ #' @param module (`teal_module`) object to be appended onto the children of `modules` |
|
| 632 | -! | +
- if (!rlang::is_missing(export) && checkmate::test_string(export, min.chars = 1)) export <- ns(export)+ #' @return A `teal_modules` object with `module` appended. |
|
| 633 |
-
+ append_module <- function(modules, module) {
|
||
| 634 | -! | +8x |
- self$wait_for_value(+ checkmate::assert_class(modules, "teal_modules") |
| 635 | -! | +6x |
- input = input,+ checkmate::assert_class(module, "teal_module") |
| 636 | -! | +4x |
- output = output,+ modules$children <- c(modules$children, list(module)) |
| 637 | -! | +4x |
- export = export,+ labels <- vapply(modules$children, function(submodule) submodule$label, character(1)) |
| 638 | -+ | 4x |
- ...+ names(modules$children) <- get_unique_labels(labels) |
| 639 | -+ | 4x |
- )+ modules |
| 640 |
- }+ } |
||
| 641 |
- ),+ |
||
| 642 |
- # private members ----+ #' Extract/Remove module(s) of specific class |
||
| 643 |
- private = list(+ #' |
||
| 644 |
- # private attributes ----+ #' Given a `teal_module` or a `teal_modules`, return the elements of the structure according to `class`. |
||
| 645 |
- data = NULL,+ #' |
||
| 646 |
- modules = NULL,+ #' @param modules (`teal_modules`) |
||
| 647 |
- filter = teal_slices(),+ #' @param class The class name of `teal_module` to be extracted or dropped. |
||
| 648 |
- ns = list(+ #' @keywords internal |
||
| 649 |
- module = character(0),+ #' @return |
||
| 650 |
- filter_panel = character(0)+ #' - For `extract_module`, a `teal_module` of class `class` or `teal_modules` containing modules of class `class`. |
||
| 651 |
- ),+ #' - For `drop_module`, the opposite, which is all `teal_modules` of class other than `class`. |
||
| 652 |
- # private methods ----+ #' @rdname module_management |
||
| 653 |
- set_active_ns = function() {
+ extract_module <- function(modules, class) {
|
||
| 654 | -! | +28x |
- all_inputs <- self$get_values()$input+ if (inherits(modules, class)) {
|
| 655 | ! |
- active_tab_inputs <- all_inputs[grepl("-active_tab$", names(all_inputs))]
+ modules |
|
| 656 | -+ | 28x |
-
+ } else if (inherits(modules, "teal_module")) {
|
| 657 | -! | +15x |
- tab_ns <- unlist(lapply(names(active_tab_inputs), function(name) {
+ NULL |
| 658 | -! | +13x |
- gsub(+ } else if (inherits(modules, "teal_modules")) {
|
| 659 | -! | +13x |
- pattern = "-active_tab$",+ Filter(function(x) length(x) > 0L, lapply(modules$children, extract_module, class)) |
| 660 | -! | +
- replacement = sprintf("-%s", active_tab_inputs[[name]]),
+ } |
|
| 661 | -! | +
- name+ } |
|
| 662 |
- )+ |
||
| 663 |
- }))+ #' @keywords internal |
||
| 664 | -! | +
- active_ns <- tab_ns[1]+ #' @return `teal_modules` |
|
| 665 | -! | +
- if (length(tab_ns) > 1) {
+ #' @rdname module_management |
|
| 666 | -! | +
- for (i in 2:length(tab_ns)) {
+ drop_module <- function(modules, class) {
|
|
| 667 | ! |
- next_ns <- tab_ns[i]+ if (inherits(modules, class)) {
|
|
| 668 | ! |
- if (grepl(pattern = active_ns, next_ns)) {
+ NULL |
|
| 669 | ! |
- active_ns <- next_ns+ } else if (inherits(modules, "teal_module")) {
|
|
| 670 | -+ | ! |
- }+ modules |
| 671 | -+ | ! |
- }+ } else if (inherits(modules, "teal_modules")) {
|
| 672 | -+ | ! |
- }+ do.call( |
| 673 | ! |
- private$ns$module <- sprintf("%s-%s", active_ns, "module")
+ "modules", |
|
| 674 | -+ | ! |
-
+ c(Filter(function(x) length(x) > 0L, lapply(modules$children, drop_module, class)), label = modules$label) |
| 675 | -! | +
- components <- c("filter_panel", "data_summary")
+ ) |
|
| 676 | -! | +
- for (component in components) {
+ } |
|
| 677 |
- 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)))
+ ## read modules ---- |
|
| 680 |
- ) {
+
|
||
| 681 | -! | +
- private$ns[[component]] <- sprintf("%s-%s", active_ns, component)
+ #' Does the object make use of the `arg` |
|
| 682 |
- } else {
+ #' |
||
| 683 | -! | +
- private$ns[[component]] <- sprintf("%s-module_%s", active_ns, component)
+ #' @param modules (`teal_module` or `teal_modules`) object |
|
| 684 |
- }+ #' @param arg (`character(1)`) names of the arguments to be checked against formals of `teal` modules. |
||
| 685 |
- }+ #' @return `logical` whether the object makes use of `arg`. |
||
| 686 |
- },+ #' @rdname is_arg_used |
||
| 687 |
- # @description+ #' @keywords internal |
||
| 688 |
- # Get the active filter values from the active filter selection of dataset from the filter panel.+ is_arg_used <- function(modules, arg) {
|
||
| 689 | -+ | 519x |
- #+ checkmate::assert_string(arg) |
| 690 | -+ | 516x |
- # @param dataset_name (character) The name of the dataset to get the filter values from.+ if (inherits(modules, "teal_modules")) {
|
| 691 | -+ | 20x |
- # @param var_name (character) The name of the variable to get the filter values from.+ any(unlist(lapply(modules$children, is_arg_used, arg))) |
| 692 | -+ | 496x |
- #+ } else if (inherits(modules, "teal_module")) {
|
| 693 | -+ | 32x |
- # @return The value of the active filter selection.+ is_arg_used(modules$server, arg) || is_arg_used(modules$ui, arg) |
| 694 | -+ | 464x |
- get_active_filter_selection = function(dataset_name, var_name) {
+ } else if (is.function(modules)) {
|
| 695 | -! | +462x |
- checkmate::check_string(dataset_name)+ isTRUE(arg %in% names(formals(modules))) |
| 696 | -! | +
- checkmate::check_string(var_name)+ } else {
|
|
| 697 | -! | +2x |
- input_id_prefix <- sprintf(+ stop("is_arg_used function not implemented for this object")
|
| 698 | -! | +
- "%s-filters-%s-filter-%s_%s-inputs",+ } |
|
| 699 | -! | +
- self$active_filters_ns(),+ } |
|
| 700 | -! | +
- dataset_name,+ |
|
| 701 | -! | +
- dataset_name,+ |
|
| 702 | -! | +
- var_name+ #' Get module depth |
|
| 703 |
- )+ #' |
||
| 704 |
-
+ #' Depth starts at 0, so a single `teal.module` has depth 0. |
||
| 705 |
- # Find the type of filter (categorical or range)+ #' Nesting it increases overall depth by 1. |
||
| 706 | -! | +
- supported_suffix <- c("selection", "selection_manual")
+ #' |
|
| 707 | -! | +
- for (suffix in supported_suffix) {
+ #' @inheritParams init |
|
| 708 | -! | +
- if (!is.null(self$get_html(sprintf("#%s-%s", input_id_prefix, suffix)))) {
+ #' @param depth optional integer determining current depth level |
|
| 709 | -! | +
- return(self$get_value(input = sprintf("%s-%s", input_id_prefix, suffix)))
+ #' |
|
| 710 |
- }+ #' @return Depth level for given module. |
||
| 711 |
- }+ #' @keywords internal |
||
| 712 |
-
+ modules_depth <- function(modules, depth = 0L) {
|
||
| 713 | -! | +12x |
- NULL # If there are not any supported filters+ checkmate::assert_multi_class(modules, c("teal_module", "teal_modules"))
|
| 714 | -+ | 12x |
- },+ checkmate::assert_int(depth, lower = 0) |
| 715 | -+ | 11x |
- # @description+ if (inherits(modules, "teal_modules")) {
|
| 716 | -+ | 4x |
- # Check if the page is stable without any `DOM` updates in the body of the app.+ max(vapply(modules$children, modules_depth, integer(1), depth = depth + 1L)) |
| 717 |
- # This is achieved by blocing the R process by sleeping until the page is unchanged till the `stability_period`.+ } else {
|
||
| 718 | -+ | 7x |
- # @param stability_period (`numeric(1)`) The time in milliseconds to wait till the page to be stable.+ depth |
| 719 |
- # @param check_interval (`numeric(1)`) The time in milliseconds to check for changes in the page.+ } |
||
| 720 |
- # The stability check is reset when a change is detected in the page after sleeping for check_interval.+ } |
||
| 721 |
- wait_for_page_stability = function(stability_period = 2000, check_interval = 200) {
+
|
||
| 722 | -! | +
- previous_content <- self$get_html("body")
+ #' Retrieve labels from `teal_modules` |
|
| 723 | -! | +
- end_time <- Sys.time() + (stability_period / 1000)+ #' |
|
| 724 |
-
+ #' @param modules (`teal_modules`) |
||
| 725 | -! | +
- repeat {
+ #' @return A `list` containing the labels of the modules. If the modules are nested, |
|
| 726 | -! | +
- Sys.sleep(check_interval / 1000)+ #' the function returns a nested `list` of labels. |
|
| 727 | -! | +
- current_content <- self$get_html("body")
+ #' @keywords internal |
|
| 728 |
-
+ module_labels <- function(modules) {
|
||
| 729 | -! | +199x |
- if (!identical(previous_content, current_content)) {
+ if (inherits(modules, "teal_modules")) {
|
| 730 | -! | +87x |
- previous_content <- current_content+ lapply(modules$children, module_labels) |
| 731 | -! | +
- end_time <- Sys.time() + (stability_period / 1000)+ } else {
|
|
| 732 | -! | +112x |
- } else if (Sys.time() >= end_time) {
+ modules$label |
| 733 | -! | +
- break+ } |
|
| 734 |
- }+ } |
||
| 735 |
- }+ |
||
| 736 |
- }+ #' Retrieve `teal_bookmarkable` attribute from `teal_modules` |
||
| 737 |
- )+ #' |
||
| 738 |
- )+ #' @param modules (`teal_modules` or `teal_module`) object+ |
+ ||
| 739 | ++ |
+ #' @return named list of the same structure as `modules` with `TRUE` or `FALSE` values indicating+ |
+ |
| 740 | ++ |
+ #' whether the module is bookmarkable.+ |
+ |
| 741 | ++ |
+ #' @keywords internal+ |
+ |
| 742 | ++ |
+ modules_bookmarkable <- function(modules) {
+ |
+ |
| 743 | +199x | +
+ checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"))
+ |
+ |
| 744 | +199x | +
+ if (inherits(modules, "teal_modules")) {
+ |
+ |
| 745 | +87x | +
+ setNames(+ |
+ |
| 746 | +87x | +
+ lapply(modules$children, modules_bookmarkable),+ |
+ |
| 747 | +87x | +
+ vapply(modules$children, `[[`, "label", FUN.VALUE = character(1))+ |
+ |
| 748 | ++ |
+ )+ |
+ |
| 749 | ++ |
+ } else {
+ |
+ |
| 750 | +112x | +
+ attr(modules, "teal_bookmarkable", exact = TRUE)+ |
+ |
| 751 | ++ |
+ }+ |
+ |
| 752 | ++ |
+ } |
| 1 |
- #' Landing popup module+ # FilteredData ------ |
||
| 2 |
- #'+ |
||
| 3 |
- #' @description Creates a landing welcome popup for `teal` applications.+ #' Drive a `teal` application |
||
| 5 |
- #' This module is used to display a popup dialog when the application starts.+ #' Extension of the `shinytest2::AppDriver` class with methods for |
||
| 6 |
- #' The dialog blocks access to the application and must be closed with a button before the application can be viewed.+ #' driving a teal application for performing interactions for `shinytest2` tests. |
||
| 8 |
- #' @param label (`character(1)`) Label of the module.+ #' @keywords internal |
||
| 9 |
- #' @param title (`character(1)`) Text to be displayed as popup title.+ #' |
||
| 10 |
- #' @param content (`character(1)`, `shiny.tag` or `shiny.tag.list`) with the content of the popup.+ TealAppDriver <- R6::R6Class( # nolint: object_name. |
||
| 11 |
- #' Passed to `...` of `shiny::modalDialog`. See examples.+ "TealAppDriver", |
||
| 12 |
- #' @param buttons (`shiny.tag` or `shiny.tag.list`) Typically a `modalButton` or `actionButton`. See examples.+ inherit = {
|
||
| 13 |
- #'+ if (!requireNamespace("shinytest2", quietly = TRUE)) {
|
||
| 14 |
- #' @return A `teal_module` (extended with `teal_landing_module` class) to be used in `teal` applications.+ stop("Please install 'shinytest2' package to use this class.")
|
||
| 15 |
- #'+ } |
||
| 16 |
- #' @examples+ if (!requireNamespace("rvest", quietly = TRUE)) {
|
||
| 17 |
- #' app1 <- init(+ stop("Please install 'rvest' package to use this class.")
|
||
| 18 |
- #' data = teal_data(iris = iris),+ } |
||
| 19 |
- #' modules = modules(+ shinytest2::AppDriver |
||
| 20 |
- #' example_module()+ }, |
||
| 21 |
- #' ),+ # public methods ---- |
||
| 22 |
- #' landing_popup = landing_popup_module(+ public = list( |
||
| 23 |
- #' content = "A place for the welcome message or a disclaimer statement.",+ #' @description |
||
| 24 |
- #' buttons = modalButton("Proceed")
+ #' Initialize a `TealAppDriver` object for testing a `teal` application. |
||
| 25 |
- #' )+ #' |
||
| 26 |
- #' )+ #' @param data,modules,filter,title,header,footer,landing_popup arguments passed to `init` |
||
| 27 |
- #' if (interactive()) {
+ #' @param timeout (`numeric`) Default number of milliseconds for any timeout or |
||
| 28 |
- #' shinyApp(app1$ui, app1$server)+ #' timeout_ parameter in the `TealAppDriver` class. |
||
| 29 |
- #' }+ #' Defaults to 20s. |
||
| 30 |
- #'+ #' |
||
| 31 |
- #' app2 <- init(+ #' See [`shinytest2::AppDriver`] `new` method for more details on how to change it |
||
| 32 |
- #' data = teal_data(iris = iris),+ #' via options or environment variables. |
||
| 33 |
- #' modules = modules(+ #' @param load_timeout (`numeric`) How long to wait for the app to load, in ms. |
||
| 34 |
- #' example_module()+ #' This includes the time to start R. Defaults to 100s. |
||
| 35 |
- #' ),+ #' |
||
| 36 |
- #' landing_popup = landing_popup_module(+ #' See [`shinytest2::AppDriver`] `new` method for more details on how to change it |
||
| 37 |
- #' title = "Welcome",+ #' via options or environment variables |
||
| 38 |
- #' content = tags$b(+ #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$new` |
||
| 39 |
- #' "A place for the welcome message or a disclaimer statement.",+ #' |
||
| 40 |
- #' style = "color: red;"+ #' |
||
| 41 |
- #' ),+ #' @return Object of class `TealAppDriver` |
||
| 42 |
- #' buttons = tagList(+ initialize = function(data, |
||
| 43 |
- #' modalButton("Proceed"),
+ modules, |
||
| 44 |
- #' actionButton("read", "Read more",
+ filter = teal_slices(), |
||
| 45 |
- #' onclick = "window.open('http://google.com', '_blank')"
+ title = build_app_title(), |
||
| 46 |
- #' ),+ header = tags$p(), |
||
| 47 |
- #' actionButton("close", "Reject", onclick = "window.close()")
+ footer = tags$p(), |
||
| 48 |
- #' )+ landing_popup = NULL, |
||
| 49 |
- #' )+ timeout = rlang::missing_arg(), |
||
| 50 |
- #' )+ load_timeout = rlang::missing_arg(), |
||
| 51 |
- #'+ ...) {
|
||
| 52 | -+ | ! |
- #' if (interactive()) {
+ private$data <- data |
| 53 | -+ | ! |
- #' shinyApp(app2$ui, app2$server)+ private$modules <- modules |
| 54 | -+ | ! |
- #' }+ private$filter <- filter |
| 55 | -+ | ! |
- #'+ app <- init( |
| 56 | -+ | ! |
- #' @export+ data = data, |
| 57 | -+ | ! |
- landing_popup_module <- function(label = "Landing Popup",+ modules = modules, |
| 58 | -+ | ! |
- title = NULL,+ filter = filter, |
| 59 | -+ | ! |
- content = NULL,+ title = title, |
| 60 | -+ | ! |
- buttons = modalButton("Accept")) {
+ header = header, |
| 61 | ! |
- checkmate::assert_string(label)+ footer = footer, |
|
| 62 | ! |
- checkmate::assert_string(title, null.ok = TRUE)+ landing_popup = landing_popup, |
|
| 63 | -! | +
- checkmate::assert_multi_class(+ ) |
|
| 64 | -! | +
- content,+ |
|
| 65 | -! | +
- classes = c("character", "shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE
+ # Default timeout is hardcoded to 4s in shinytest2:::resolve_timeout |
|
| 66 |
- )+ # It must be set as parameter to the AppDriver |
||
| 67 | ! |
- checkmate::assert_multi_class(buttons, classes = c("shiny.tag", "shiny.tag.list"))
+ suppressWarnings( |
|
| 68 | -+ | ! |
-
+ super$initialize( |
| 69 | ! |
- message("Initializing landing_popup_module")
+ app_dir = shinyApp(app$ui, app$server), |
|
| 70 | -+ | ! |
-
+ name = "teal", |
| 71 | ! |
- module <- module(+ variant = shinytest2::platform_variant(), |
|
| 72 | ! |
- label = label,+ timeout = rlang::maybe_missing(timeout, 20 * 1000), |
|
| 73 | ! |
- server = function(id) {
+ load_timeout = rlang::maybe_missing(load_timeout, 100 * 1000), |
|
| 74 | -! | +
- moduleServer(id, function(input, output, session) {
+ ... |
|
| 75 | -! | +
- showModal(+ ) |
|
| 76 | -! | +
- modalDialog(+ ) |
|
| 77 | ++ | + + | +|
| 78 | ++ |
+ # Check for minimum version of Chrome that supports the tests+ |
+ |
| 79 | ++ |
+ # - Element.checkVisibility was added on 105+ |
+ |
| 80 | ! |
- id = "landingpopup",+ chrome_version <- numeric_version( |
|
| 78 | +81 | ! |
- title = title,+ gsub( |
| 79 | +82 | ! |
- content,+ "[[:alnum:]_]+/", # Prefix that ends with forward slash+ |
+
| 83 | ++ |
+ "", |
|
| 80 | +84 | ! |
- footer = buttons+ self$get_chromote_session()$Browser$getVersion()$product |
| 81 | +85 |
- )+ ),+ |
+ |
| 86 | +! | +
+ strict = FALSE |
|
| 82 | +87 |
- )+ ) |
|
| 83 | +88 |
- })+ + |
+ |
| 89 | +! | +
+ required_version <- "121" |
|
| 84 | +90 |
- }+ + |
+ |
| 91 | +! | +
+ testthat::skip_if(+ |
+ |
| 92 | +! | +
+ is.na(chrome_version),+ |
+ |
| 93 | +! | +
+ "Problem getting Chrome version, please contact the developers." |
|
| 85 | +94 |
- )+ ) |
|
| 86 | +95 | ! |
- class(module) <- c("teal_module_landing", class(module))
+ testthat::skip_if( |
| 87 | +96 | ! |
- module+ chrome_version < required_version,+ |
+
| 97 | +! | +
+ sprintf(+ |
+ |
| 98 | +! | +
+ "Chrome version '%s' is not supported, please upgrade to '%s' or higher",+ |
+ |
| 99 | +! | +
+ chrome_version,+ |
+ |
| 100 | +! | +
+ required_version |
|
| 88 | +101 |
- }+ ) |
| 1 | +102 |
- #' App state management.+ ) |
|
| 2 | +103 |
- #'+ # end od check |
|
| 3 | +104 |
- #' @description+ + |
+ |
| 105 | +! | +
+ private$set_active_ns()+ |
+ |
| 106 | +! | +
+ self$wait_for_idle() |
|
| 4 | +107 |
- #' `r lifecycle::badge("experimental")`
+ }, |
|
| 5 | +108 |
- #'+ #' @description |
|
| 6 | +109 |
- #' Capture and restore the global (app) input state.+ #' Append parent [`shinytest2::AppDriver`] `click` method with a call to `waif_for_idle()` method. |
|
| 7 | +110 |
- #'+ #' @param ... arguments passed to parent [`shinytest2::AppDriver`] `click()` method. |
|
| 8 | +111 |
- #' @details+ click = function(...) {
+ |
+ |
| 112 | +! | +
+ super$click(...)+ |
+ |
| 113 | +! | +
+ private$wait_for_page_stability() |
|
| 9 | +114 |
- #' This module introduces bookmarks into `teal` apps: the `shiny` bookmarking mechanism becomes enabled+ }, |
|
| 10 | +115 |
- #' and server-side bookmarks can be created.+ #' @description |
|
| 11 | +116 |
- #'+ #' Check if the app has shiny errors. This checks for global shiny errors. |
|
| 12 | +117 |
- #' The bookmark manager presents a button with the bookmark icon and is placed in the tab-bar.+ #' Note that any shiny errors dependent on shiny server render will only be captured after the teal module tab |
|
| 13 | +118 |
- #' When clicked, the button creates a bookmark and opens a modal which displays the bookmark URL.+ #' is visited because shiny will not trigger server computations when the tab is invisible. |
|
| 14 | +119 |
- #'+ #' So, navigate to the module tab you want to test before calling this function. |
|
| 15 | +120 |
- #' `teal` does not guarantee that all modules (`teal_module` objects) are bookmarkable.+ #' Although, this catches errors hidden in the other module tabs if they are already rendered. |
|
| 16 | +121 |
- #' Those that are, have a `teal_bookmarkable` attribute set to `TRUE`. If any modules are not bookmarkable,+ expect_no_shiny_error = function() {
+ |
+ |
| 122 | +! | +
+ testthat::expect_null(+ |
+ |
| 123 | +! | +
+ self$get_html(".shiny-output-error:not(.shiny-output-error-validation)"),
+ |
+ |
| 124 | +! | +
+ info = "Shiny error is observed" |
|
| 17 | +125 |
- #' the bookmark manager modal displays a warning and the bookmark button displays a flag.+ ) |
|
| 18 | +126 |
- #' In order to communicate that a external module is bookmarkable, the module developer+ }, |
|
| 19 | +127 |
- #' should set the `teal_bookmarkable` attribute to `TRUE`.+ #' @description |
|
| 20 | +128 |
- #'+ #' Check if the app has no validation errors. This checks for global shiny validation errors. |
|
| 21 | +129 |
- #' @section Server logic:+ expect_no_validation_error = function() {
+ |
+ |
| 130 | +! | +
+ testthat::expect_null(+ |
+ |
| 131 | +! | +
+ self$get_html(".shiny-output-error-validation"),
+ |
+ |
| 132 | +! | +
+ info = "No validation error is observed" |
|
| 22 | +133 |
- #' A bookmark is a URL that contains the app address with a `/?_state_id_=<bookmark_dir>` suffix.+ ) |
|
| 23 | +134 |
- #' `<bookmark_dir>` is a directory created on the server, where the state of the application is saved.+ }, |
|
| 24 | +135 |
- #' Accessing the bookmark URL opens a new session of the app that starts in the previously saved state.+ #' @description |
|
| 25 | +136 |
- #'+ #' Check if the app has validation errors. This checks for global shiny validation errors. |
|
| 26 | +137 |
- #' @section Note:+ expect_validation_error = function() {
+ |
+ |
| 138 | +! | +
+ testthat::expect_false(+ |
+ |
| 139 | +! | +
+ is.null(self$get_html(".shiny-output-error-validation")),
+ |
+ |
| 140 | +! | +
+ info = "Validation error is not observed" |
|
| 27 | +141 |
- #' To enable bookmarking use either:+ ) |
|
| 28 | +142 |
- #' - `shiny` app by using `shinyApp(..., enableBookmarking = "server")` (not supported in `shinytest2`)+ }, |
|
| 29 | +143 |
- #' - set `options(shiny.bookmarkStore = "server")` before running the app+ #' @description |
|
| 30 | +144 |
- #'+ #' Set the input in the `teal` app. |
|
| 31 | +145 |
- #'+ #' |
|
| 32 | +146 |
- #' @inheritParams init+ #' @param input_id (character) The shiny input id with it's complete name space.+ |
+ |
| 147 | ++ |
+ #' @param value The value to set the input to. |
|
| 33 | +148 |
- #'+ #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$set_inputs` |
|
| 34 | +149 |
- #' @return Invisible `NULL`.+ #' |
|
| 35 | +150 |
- #'+ #' @return The `TealAppDriver` object invisibly. |
|
| 36 | +151 |
- #' @aliases bookmark bookmark_manager bookmark_manager_module+ set_input = function(input_id, value, ...) {
|
|
| 37 | -+ | ||
| 152 | +! |
- #'+ do.call( |
|
| 38 | -+ | ||
| 153 | +! |
- #' @name module_bookmark_manager+ self$set_inputs, |
|
| 39 | -+ | ||
| 154 | +! |
- #' @rdname module_bookmark_manager+ c(setNames(list(value), input_id), list(...)) |
|
| 40 | +155 |
- #'+ ) |
|
| 41 | -+ | ||
| 156 | +! |
- #' @keywords internal+ invisible(self) |
|
| 42 | +157 |
- #'+ }, |
|
| 43 | +158 |
- NULL+ #' @description |
|
| 44 | +159 |
-
+ #' Navigate the teal tabs in the `teal` app. |
|
| 45 | +160 |
- #' @rdname module_bookmark_manager+ #' |
|
| 46 | +161 |
- ui_bookmark_panel <- function(id, modules) {
+ #' @param tabs (character) Labels of tabs to navigate to. The order of the tabs is important, |
|
| 47 | -! | +||
| 162 | +
- ns <- NS(id)+ #' and it should start with the most parent level tab. |
||
| 48 | +163 |
-
+ #' Note: In case the teal tab group has duplicate names, the first tab will be selected, |
|
| 49 | -! | +||
| 164 | +
- bookmark_option <- get_bookmarking_option()+ #' If you wish to select the second tab with the same name, use the suffix "_1". |
||
| 50 | -! | +||
| 165 | +
- is_unbookmarkable <- need_bookmarking(modules)+ #' If you wish to select the third tab with the same name, use the suffix "_2" and so on. |
||
| 51 | -! | +||
| 166 | +
- shinyOptions(bookmarkStore = bookmark_option)+ #' |
||
| 52 | +167 |
-
+ #' @return The `TealAppDriver` object invisibly. |
|
| 53 | +168 |
- # Render bookmark warnings count+ navigate_teal_tab = function(tabs) {
|
|
| 54 | +169 | ! |
- if (!all(is_unbookmarkable) && identical(bookmark_option, "server")) {
+ checkmate::check_character(tabs, min.len = 1) |
| 55 | +170 | ! |
- tags$button(+ for (tab in tabs) {
|
| 56 | +171 | ! |
- id = ns("do_bookmark"),
+ self$set_input( |
| 57 | +172 | ! |
- class = "btn action-button wunder_bar_button bookmark_manager_button",+ "teal-teal_modules-active_tab", |
| 58 | +173 | ! |
- title = "Add bookmark",+ get_unique_labels(tab), |
| 59 | +174 | ! |
- tags$span(+ wait_ = FALSE |
| 60 | -! | +||
| 175 | +
- suppressMessages(icon("fas fa-bookmark")),
+ ) |
||
| 61 | -! | +||
| 176 | +
- if (any(is_unbookmarkable)) {
+ } |
||
| 62 | +177 | ! |
- tags$span(+ self$wait_for_idle() |
| 63 | +178 | ! |
- sum(is_unbookmarkable),+ private$set_active_ns() |
| 64 | +179 | ! |
- class = "badge-warning badge-count text-white bg-danger"+ invisible(self) |
| 65 | +180 |
- )+ }, |
|
| 66 | +181 |
- }+ #' @description |
|
| 67 | +182 |
- )+ #' Get the active shiny name space for different components of the teal app. |
|
| 68 | +183 |
- )+ #' |
|
| 69 | +184 |
- }+ #' @return (`list`) The list of active shiny name space of the teal components. |
|
| 70 | +185 |
- }+ active_ns = function() {
|
|
| 71 | -+ | ||
| 186 | +! |
-
+ if (identical(private$ns$module, character(0))) {
|
|
| 72 | -+ | ||
| 187 | +! |
- #' @rdname module_bookmark_manager+ private$set_active_ns() |
|
| 73 | +188 |
- srv_bookmark_panel <- function(id, modules) {
- |
- |
| 74 | -87x | -
- checkmate::assert_character(id)- |
- |
| 75 | -87x | -
- checkmate::assert_class(modules, "teal_modules")- |
- |
| 76 | -87x | -
- moduleServer(id, function(input, output, session) {
- |
- |
| 77 | -87x | -
- logger::log_debug("bookmark_manager_srv initializing")
- |
- |
| 78 | -87x | -
- ns <- session$ns- |
- |
| 79 | -87x | -
- bookmark_option <- get_bookmarking_option()+ } |
|
| 80 | -87x | +||
| 189 | +! |
- is_unbookmarkable <- need_bookmarking(modules)+ private$ns |
|
| 81 | +190 |
-
+ }, |
|
| 82 | +191 |
- # Set up bookmarking callbacks ----+ #' @description |
|
| 83 | +192 |
- # Register bookmark exclusions: do_bookmark button to avoid re-bookmarking- |
- |
| 84 | -87x | -
- setBookmarkExclude(c("do_bookmark"))
+ #' Get the active shiny name space for interacting with the module content. |
|
| 85 | +193 |
- # This bookmark can only be used on the app session.+ #' |
|
| 86 | -87x | +||
| 194 | +
- app_session <- .subset2(session, "parent")+ #' @return (`string`) The active shiny name space of the component. |
||
| 87 | -87x | +||
| 195 | +
- app_session$onBookmarked(function(url) {
+ active_module_ns = function() {
|
||
| 88 | +196 | ! |
- logger::log_debug("bookmark_manager_srv@onBookmarked: bookmark button clicked, registering bookmark")
+ if (identical(private$ns$module, character(0))) {
|
| 89 | +197 | ! |
- modal_content <- if (bookmark_option != "server") {
+ private$set_active_ns() |
| 90 | -! | +||
| 198 | +
- msg <- sprintf(+ } |
||
| 91 | +199 | ! |
- "Bookmarking has been set to \"%s\".\n%s\n%s",+ private$ns$module |
| 92 | -! | +||
| 200 | +
- bookmark_option,+ }, |
||
| 93 | -! | +||
| 201 | +
- "Only server-side bookmarking is supported.",+ #' @description |
||
| 94 | -! | +||
| 202 | +
- "Please contact your app developer."+ #' Get the active shiny name space bound with a custom `element` name. |
||
| 95 | +203 |
- )+ #' |
|
| 96 | -! | +||
| 204 | +
- tags$div(+ #' @param element `character(1)` custom element name. |
||
| 97 | -! | +||
| 205 | +
- tags$p(msg, class = "text-warning")+ #' |
||
| 98 | +206 |
- )+ #' @return (`string`) The active shiny name space of the component bound with the input `element`. |
|
| 99 | +207 |
- } else {
+ active_module_element = function(element) {
|
|
| 100 | +208 | ! |
- tags$div(+ checkmate::assert_string(element) |
| 101 | +209 | ! |
- tags$span(+ sprintf("#%s-%s", self$active_module_ns(), element)
|
| 102 | -! | +||
| 210 | +
- tags$pre(url)+ }, |
||
| 103 | +211 |
- ),+ #' @description |
|
| 104 | -! | +||
| 212 | +
- if (any(is_unbookmarkable)) {
+ #' Get the text of the active shiny name space bound with a custom `element` name. |
||
| 105 | -! | +||
| 213 | +
- bkmb_summary <- rapply2(+ #' |
||
| 106 | -! | +||
| 214 | +
- modules_bookmarkable(modules),+ #' @param element `character(1)` the text of the custom element name. |
||
| 107 | -! | +||
| 215 | +
- function(x) {
+ #' |
||
| 108 | -! | +||
| 216 | +
- if (isTRUE(x)) {
+ #' @return (`string`) The text of the active shiny name space of the component bound with the input `element`. |
||
| 109 | -! | +||
| 217 | +
- "\u2705" # check mark+ active_module_element_text = function(element) {
|
||
| 110 | +218 | ! |
- } else if (isFALSE(x)) {
+ checkmate::assert_string(element) |
| 111 | +219 | ! |
- "\u274C" # cross mark+ self$get_text(self$active_module_element(element)) |
| 112 | +220 |
- } else {
- |
- |
| 113 | -! | -
- "\u2753" # question mark+ }, |
|
| 114 | +221 |
- }+ #' @description |
|
| 115 | +222 |
- }+ #' Get the active shiny name space for interacting with the filter panel. |
|
| 116 | +223 |
- )- |
- |
| 117 | -! | -
- tags$div(- |
- |
| 118 | -! | -
- tags$p(- |
- |
| 119 | -! | -
- icon("fas fa-exclamation-triangle"),
+ #' |
|
| 120 | -! | +||
| 224 | +
- "Some modules will not be restored when using this bookmark.",+ #' @return (`string`) The active shiny name space of the component. |
||
| 121 | -! | +||
| 225 | +
- tags$br(),+ active_filters_ns = function() {
|
||
| 122 | +226 | ! |
- "Check the list below to see which modules are not bookmarkable.",+ if (identical(private$ns$filter_panel, character(0))) {
|
| 123 | +227 | ! |
- class = "text-warning"+ private$set_active_ns() |
| 124 | +228 |
- ),+ } |
|
| 125 | +229 | ! |
- tags$pre(yaml::as.yaml(bkmb_summary))+ private$ns$filter_panel |
| 126 | +230 |
- )+ }, |
|
| 127 | +231 |
- }+ #' @description |
|
| 128 | +232 |
- )+ #' Get the active shiny name space for interacting with the data-summary panel. |
|
| 129 | +233 |
- }+ #' |
|
| 130 | +234 |
-
+ #' @return (`string`) The active shiny name space of the data-summary component. |
|
| 131 | -! | +||
| 235 | +
- showModal(+ active_data_summary_ns = function() {
|
||
| 132 | +236 | ! |
- modalDialog(+ if (identical(private$ns$data_summary, character(0))) {
|
| 133 | +237 | ! |
- id = ns("bookmark_modal"),
+ private$set_active_ns() |
| 134 | -! | +||
| 238 | +
- title = "Bookmarked teal app url",+ } |
||
| 135 | +239 | ! |
- modal_content,+ private$ns$data_summary |
| 136 | -! | +||
| 240 | +
- easyClose = TRUE+ }, |
||
| 137 | +241 |
- )+ #' @description |
|
| 138 | +242 |
- )+ #' Get the active shiny name space bound with a custom `element` name. |
|
| 139 | +243 |
- })+ #' |
|
| 140 | +244 |
-
+ #' @param element `character(1)` custom element name. |
|
| 141 | +245 |
- # manually trigger bookmarking because of the problems reported on windows with bookmarkButton in teal+ #' |
|
| 142 | -87x | +||
| 246 | +
- observeEvent(input$do_bookmark, {
+ #' @return (`string`) The active shiny name space of the component bound with the input `element`.+ |
+ ||
| 247 | ++ |
+ active_data_summary_element = function(element) {
|
|
| 143 | +248 | ! |
- logger::log_debug("bookmark_manager_srv@1 do_bookmark module clicked.")
+ checkmate::assert_string(element) |
| 144 | +249 | ! |
- session$doBookmark()+ sprintf("#%s-%s", self$active_data_summary_ns(), element)
|
| 145 | +250 |
- })+ }, |
|
| 146 | +251 |
-
+ #' @description |
|
| 147 | -87x | +||
| 252 | +
- invisible(NULL)+ #' Get the input from the module in the `teal` app. |
||
| 148 | +253 |
- })+ #' This function will only access inputs from the name space of the current active teal module. |
|
| 149 | +254 |
- }+ #' |
|
| 150 | +255 |
-
+ #' @param input_id (character) The shiny input id to get the value from. |
|
| 151 | +256 |
-
+ #' |
|
| 152 | +257 |
- #' @rdname module_bookmark_manager+ #' @return The value of the shiny input. |
|
| 153 | +258 |
- get_bookmarking_option <- function() {
+ get_active_module_input = function(input_id) {
|
|
| 154 | -87x | +||
| 259 | +! |
- bookmark_option <- getShinyOption("bookmarkStore")
+ checkmate::check_string(input_id) |
|
| 155 | -87x | +||
| 260 | +! |
- if (is.null(bookmark_option) && identical(getOption("shiny.bookmarkStore"), "server")) {
+ self$get_value(input = sprintf("%s-%s", self$active_module_ns(), input_id))
|
|
| 156 | -! | +||
| 261 | +
- bookmark_option <- getOption("shiny.bookmarkStore")
+ }, |
||
| 157 | +262 |
- }+ #' @description |
|
| 158 | -87x | +||
| 263 | +
- bookmark_option+ #' Get the output from the module in the `teal` app. |
||
| 159 | +264 |
- }+ #' This function will only access outputs from the name space of the current active teal module. |
|
| 160 | +265 |
-
+ #' |
|
| 161 | +266 |
- #' @rdname module_bookmark_manager+ #' @param output_id (character) The shiny output id to get the value from. |
|
| 162 | +267 |
- need_bookmarking <- function(modules) {
+ #' |
|
| 163 | -87x | +||
| 268 | +
- unlist(rapply2(+ #' @return The value of the shiny output. |
||
| 164 | -87x | +||
| 269 | +
- modules_bookmarkable(modules),+ get_active_module_output = function(output_id) {
|
||
| 165 | -87x | +||
| 270 | +! |
- Negate(isTRUE)+ checkmate::check_string(output_id) |
|
| 166 | -+ | ||
| 271 | +! |
- ))+ self$get_value(output = sprintf("%s-%s", self$active_module_ns(), output_id))
|
|
| 167 | +272 |
- }+ }, |
|
| 168 | +273 |
-
+ #' @description |
|
| 169 | +274 |
-
+ #' Get the output from the module's `teal.widgets::table_with_settings` or `DT::DTOutput` in the `teal` app. |
|
| 170 | +275 |
- # utilities ----+ #' This function will only access outputs from the name space of the current active teal module. |
|
| 171 | +276 |
-
+ #' |
|
| 172 | +277 |
- #' Restore value from bookmark.+ #' @param table_id (`character(1)`) The id of the table in the active teal module's name space. |
|
| 173 | +278 |
- #'+ #' @param which (integer) If there is more than one table, which should be extracted. |
|
| 174 | +279 |
- #' Get value from bookmark or return default.+ #' By default it will look for a table that is built using `teal.widgets::table_with_settings`. |
|
| 175 | +280 |
- #'+ #' |
|
| 176 | +281 |
- #' Bookmarks can store not only inputs but also arbitrary values.+ #' @return The data.frame with table contents. |
|
| 177 | +282 |
- #' These values are stored by `onBookmark` callbacks and restored by `onBookmarked` callbacks,+ get_active_module_table_output = function(table_id, which = 1) {
|
|
| 178 | -+ | ||
| 283 | +! |
- #' and they are placed in the `values` environment in the `session$restoreContext` field.+ checkmate::check_number(which, lower = 1) |
|
| 179 | -+ | ||
| 284 | +! |
- #' Using `teal_data_module` makes it impossible to run the callbacks+ checkmate::check_string(table_id) |
|
| 180 | -+ | ||
| 285 | +! |
- #' because the app becomes ready before modules execute and callbacks are registered.+ table <- rvest::html_table( |
|
| 181 | -+ | ||
| 286 | +! |
- #' In those cases the stored values can still be recovered from the `session` object directly.+ self$get_html_rvest(self$active_module_element(table_id)), |
|
| 182 | -+ | ||
| 287 | +! |
- #'+ fill = TRUE |
|
| 183 | +288 |
- #' Note that variable names in the `values` environment are prefixed with module name space names,+ ) |
|
| 184 | -+ | ||
| 289 | +! |
- #' therefore, when using this function in modules, `value` must be run through the name space function.+ if (length(table) == 0) {
|
|
| 185 | -+ | ||
| 290 | +! |
- #'+ data.frame() |
|
| 186 | +291 |
- #' @param value (`character(1)`) name of value to restore+ } else {
+ |
+ |
| 292 | +! | +
+ table[[which]] |
|
| 187 | +293 |
- #' @param default fallback value+ } |
|
| 188 | +294 |
- #'+ }, |
|
| 189 | +295 |
- #' @return+ #' @description |
|
| 190 | +296 |
- #' In an application restored from a server-side bookmark,+ #' Get the output from the module's `teal.widgets::plot_with_settings` in the `teal` app. |
|
| 191 | +297 |
- #' the variable specified by `value` from the `values` environment.+ #' This function will only access plots from the name space of the current active teal module. |
|
| 192 | +298 |
- #' Otherwise `default`.+ #' |
|
| 193 | +299 |
- #'+ #' @param plot_id (`character(1)`) The id of the plot in the active teal module's name space. |
|
| 194 | +300 |
- #' @keywords internal+ #' |
|
| 195 | +301 |
- #'+ #' @return The `src` attribute as `character(1)` vector. |
|
| 196 | +302 |
- restoreValue <- function(value, default) { # nolint: object_name.
+ get_active_module_plot_output = function(plot_id) {
|
|
| 197 | -174x | +||
| 303 | +! |
- checkmate::assert_character("value")
+ checkmate::check_string(plot_id) |
|
| 198 | -174x | +||
| 304 | +! |
- session_default <- shiny::getDefaultReactiveDomain()+ self$get_attr( |
|
| 199 | -174x | +||
| 305 | +! |
- session_parent <- .subset2(session_default, "parent")+ self$active_module_element(sprintf("%s-plot_main > img", plot_id)),
|
|
| 200 | -174x | +||
| 306 | +! |
- session <- if (is.null(session_parent)) session_default else session_parent+ "src" |
|
| 201 | +307 |
-
+ ) |
|
| 202 | -174x | +||
| 308 | +
- if (isTRUE(session$restoreContext$active) && exists(value, session$restoreContext$values, inherits = FALSE)) {
+ }, |
||
| 203 | -! | +||
| 309 | +
- session$restoreContext$values[[value]]+ #' @description |
||
| 204 | +310 |
- } else {
+ #' Set the input in the module in the `teal` app. |
|
| 205 | -174x | +||
| 311 | +
- default+ #' This function will only set inputs in the name space of the current active teal module. |
||
| 206 | +312 |
- }+ #' |
|
| 207 | +313 |
- }+ #' @param input_id (character) The shiny input id to get the value from. |
|
| 208 | +314 |
-
+ #' @param value The value to set the input to. |
|
| 209 | +315 |
- #' Compare bookmarks.+ #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$set_inputs`+ |
+ |
| 316 | ++ |
+ #'+ |
+ |
| 317 | ++ |
+ #' @return The `TealAppDriver` object invisibly.+ |
+ |
| 318 | ++ |
+ set_active_module_input = function(input_id, value, ...) {
+ |
+ |
| 319 | +! | +
+ checkmate::check_string(input_id)+ |
+ |
| 320 | +! | +
+ checkmate::check_string(value)+ |
+ |
| 321 | +! | +
+ self$set_input( |
|
| 210 | -+ | ||
| 322 | +! |
- #'+ sprintf("%s-%s", self$active_module_ns(), input_id),
|
|
| 211 | -+ | ||
| 323 | +! |
- #' Test if two bookmarks store identical state.+ value, |
|
| 212 | +324 |
- #'+ ... |
|
| 213 | +325 |
- #' `input` environments are compared one variable at a time and if not identical,+ ) |
|
| 214 | -+ | ||
| 326 | +! |
- #' values in both bookmarks are reported. States of `datatable`s are stripped+ dots <- rlang::list2(...) |
|
| 215 | -+ | ||
| 327 | +! |
- #' of the `time` element before comparing because the time stamp is always different.+ if (!isFALSE(dots[["wait"]])) self$wait_for_idle() # Default behavior is to wait |
|
| 216 | -+ | ||
| 328 | +! |
- #' The contents themselves are not printed as they are large and the contents are not informative.+ invisible(self) |
|
| 217 | +329 |
- #' Elements present in one bookmark and absent in the other are also reported.+ }, |
|
| 218 | +330 |
- #' Differences are printed as messages.+ #' @description |
|
| 219 | +331 |
- #'+ #' Get the active datasets that can be accessed via the filter panel of the current active teal module. |
|
| 220 | +332 |
- #' `values` environments are compared with `all.equal`.+ get_active_filter_vars = function() {
|
|
| 221 | -+ | ||
| 333 | +! |
- #'+ displayed_datasets_index <- self$is_visible( |
|
| 222 | -+ | ||
| 334 | +! |
- #' @section How to use:+ sprintf("#%s-filters-filter_active_vars_contents > span", self$active_filters_ns())
|
|
| 223 | +335 |
- #' Open an application, change relevant inputs (typically, all of them), and create a bookmark.+ ) |
|
| 224 | +336 |
- #' Then open that bookmark and immediately create a bookmark of that.+ |
|
| 225 | -+ | ||
| 337 | +! |
- #' If restoring bookmarks occurred properly, the two bookmarks should store the same state.+ available_datasets <- self$get_text( |
|
| 226 | -+ | ||
| 338 | +! |
- #'+ sprintf( |
|
| 227 | -+ | ||
| 339 | +! |
- #'+ "#%s-filters-filter_active_vars_contents .filter_panel_dataname", |
|
| 228 | -+ | ||
| 340 | +! |
- #' @param book1,book2 bookmark directories stored in `shiny_bookmarks/`;+ self$active_filters_ns() |
|
| 229 | +341 |
- #' default to the two most recently modified directories+ ) |
|
| 230 | +342 |
- #'+ ) |
|
| 231 | +343 |
- #' @return+ |
|
| 232 | -+ | ||
| 344 | +! |
- #' Invisible `NULL` if bookmarks are identical or if there are no bookmarks to test.+ available_datasets[displayed_datasets_index] |
|
| 233 | +345 |
- #' `FALSE` if inconsistencies are detected.+ }, |
|
| 234 | +346 |
- #'+ #' @description |
|
| 235 | +347 |
- #' @keywords internal+ #' Get the active data summary table |
|
| 236 | +348 |
- #'+ #' @return `data.frame` |
|
| 237 | +349 |
- bookmarks_identical <- function(book1, book2) {
+ get_active_data_summary_table = function() {
|
|
| 238 | +350 | ! |
- if (!dir.exists("shiny_bookmarks")) {
+ summary_table <- rvest::html_table( |
| 239 | +351 | ! |
- message("no bookmark directory")
+ self$get_html_rvest(self$active_data_summary_element("table")),
|
| 240 | +352 | ! |
- return(invisible(NULL))+ fill = TRUE |
| 241 | -+ | ||
| 353 | +! |
- }+ )[[1]] |
|
| 242 | +354 | ||
| 243 | +355 | ! |
- ans <- TRUE- |
-
| 244 | -- |
-
+ col_names <- unlist(summary_table[1, ], use.names = FALSE) |
|
| 245 | +356 | ! |
- if (missing(book1) && missing(book2)) {
+ summary_table <- summary_table[-1, ] |
| 246 | +357 | ! |
- dirs <- list.dirs("shiny_bookmarks", recursive = FALSE)
+ colnames(summary_table) <- col_names |
| 247 | +358 | ! |
- bookmarks_sorted <- basename(rev(dirs[order(file.mtime(dirs))]))+ if (nrow(summary_table) > 0) {
|
| 248 | +359 | ! |
- if (length(bookmarks_sorted) < 2L) {
+ summary_table |
| 249 | -! | +||
| 360 | +
- message("no bookmarks to compare")
+ } else {
|
||
| 250 | +361 | ! |
- return(invisible(NULL))+ NULL |
| 251 | +362 |
- }+ } |
|
| 252 | -! | +||
| 363 | +
- book1 <- bookmarks_sorted[2L]+ }, |
||
| 253 | -! | +||
| 364 | +
- book2 <- bookmarks_sorted[1L]+ #' @description |
||
| 254 | +365 |
- } else {
+ #' Test if `DOM` elements are visible on the page with a JavaScript call. |
|
| 255 | -! | +||
| 366 | +
- if (!dir.exists(file.path("shiny_bookmarks", book1))) stop(book1, " not found")
+ #' @param selector (`character(1)`) `CSS` selector to check visibility. |
||
| 256 | -! | +||
| 367 | +
- if (!dir.exists(file.path("shiny_bookmarks", book2))) stop(book2, " not found")
+ #' A `CSS` id will return only one element if the UI is well formed. |
||
| 257 | +368 |
- }+ #' @param content_visibility_auto,opacity_property,visibility_property (`logical(1)`) See more information |
|
| 258 | +369 |
-
+ #' on <https://developer.mozilla.org/en-US/docs/Web/API/Element/checkVisibility>. |
|
| 259 | -! | +||
| 370 | +
- book1_input <- readRDS(file.path("shiny_bookmarks", book1, "input.rds"))
+ #' |
||
| 260 | -! | +||
| 371 | +
- book2_input <- readRDS(file.path("shiny_bookmarks", book2, "input.rds"))
+ #' @return Logical vector with all occurrences of the selector. |
||
| 261 | +372 |
-
+ is_visible = function(selector, |
|
| 262 | -! | +||
| 373 | +
- elements_common <- intersect(names(book1_input), names(book2_input))+ content_visibility_auto = FALSE, |
||
| 263 | -! | +||
| 374 | +
- dt_states <- grepl("_state$", elements_common)
+ opacity_property = FALSE, |
||
| 264 | -! | +||
| 375 | +
- if (any(dt_states)) {
+ visibility_property = FALSE) {
|
||
| 265 | +376 | ! |
- for (el in elements_common[dt_states]) {
+ checkmate::assert_string(selector) |
| 266 | +377 | ! |
- book1_input[[el]][["time"]] <- NULL+ checkmate::assert_flag(content_visibility_auto) |
| 267 | +378 | ! |
- book2_input[[el]][["time"]] <- NULL- |
-
| 268 | -- |
- }+ checkmate::assert_flag(opacity_property) |
|
| 269 | -+ | ||
| 379 | +! |
- }+ checkmate::assert_flag(visibility_property) |
|
| 270 | +380 | ||
| 271 | -! | -
- identicals <- mapply(identical, book1_input[elements_common], book2_input[elements_common])- |
- |
| 272 | +381 | ! |
- non_identicals <- names(identicals[!identicals])+ private$wait_for_page_stability() |
| 273 | -! | +||
| 382 | +
- compares <- sprintf("$ %s:\t%s --- %s", non_identicals, book1_input[non_identicals], book2_input[non_identicals])
+
|
||
| 274 | +383 | ! |
- if (length(compares) != 0L) {
+ testthat::skip_if_not( |
| 275 | +384 | ! |
- message("common elements not identical: \n", paste(compares, collapse = "\n"))
+ self$get_js("typeof Element.prototype.checkVisibility === 'function'"),
|
| 276 | +385 | ! |
- ans <- FALSE+ "Element.prototype.checkVisibility is not supported in the current browser." |
| 277 | +386 |
- }+ ) |
|
| 278 | +387 | ||
| 279 | -! | -
- elements_boook1 <- setdiff(names(book1_input), names(book2_input))- |
- |
| 280 | +388 | ! |
- if (length(elements_boook1) != 0L) {
+ unlist( |
| 281 | +389 | ! |
- dt_states <- grepl("_state$", elements_boook1)
+ self$get_js( |
| 282 | +390 | ! |
- if (any(dt_states)) {
+ sprintf( |
| 283 | +391 | ! |
- for (el in elements_boook1[dt_states]) {
+ "Array.from(document.querySelectorAll('%s')).map(el => el.checkVisibility({%s, %s, %s}))",
|
| 284 | +392 | ! |
- if (is.list(book1_input[[el]])) book1_input[[el]] <- "--- data table state ---"- |
-
| 285 | -- |
- }+ selector, |
|
| 286 | +393 |
- }+ # Extra parameters |
|
| 287 | +394 | ! |
- excess1 <- sprintf("$ %s:\t%s", elements_boook1, book1_input[elements_boook1])
+ sprintf("contentVisibilityAuto: %s", tolower(content_visibility_auto)),
|
| 288 | +395 | ! |
- message("elements only in book1: \n", paste(excess1, collapse = "\n"))
+ sprintf("opacityProperty: %s", tolower(opacity_property)),
|
| 289 | +396 | ! |
- ans <- FALSE+ sprintf("visibilityProperty: %s", tolower(visibility_property))
|
| 290 | +397 |
- }+ ) |
|
| 291 | +398 |
-
+ ) |
|
| 292 | -! | +||
| 399 | +
- elements_boook2 <- setdiff(names(book2_input), names(book1_input))+ ) |
||
| 293 | -! | +||
| 400 | +
- if (length(elements_boook2) != 0L) {
+ }, |
||
| 294 | -! | +||
| 401 | +
- dt_states <- grepl("_state$", elements_boook1)
+ #' @description |
||
| 295 | -! | +||
| 402 | +
- if (any(dt_states)) {
+ #' Get the active filter variables from a dataset in the `teal` app. |
||
| 296 | -! | +||
| 403 | +
- for (el in elements_boook1[dt_states]) {
+ #' |
||
| 297 | -! | +||
| 404 | +
- if (is.list(book2_input[[el]])) book2_input[[el]] <- "--- data table state ---"+ #' @param dataset_name (character) The name of the dataset to get the filter variables from. |
||
| 298 | +405 |
- }+ #' If `NULL`, the filter variables for all the datasets will be returned in a list. |
|
| 299 | +406 |
- }+ get_active_data_filters = function(dataset_name = NULL) {
|
|
| 300 | +407 | ! |
- excess2 <- sprintf("$ %s:\t%s", elements_boook2, book2_input[elements_boook2])
+ checkmate::check_string(dataset_name, null.ok = TRUE)+ |
+
| 408 | +! | +
+ datasets <- self$get_active_filter_vars()+ |
+ |
| 409 | +! | +
+ checkmate::assert_subset(dataset_name, datasets) |
|
| 301 | +410 | ! |
- message("elements only in book2: \n", paste(excess2, collapse = "\n"))
+ active_filters <- lapply( |
| 302 | +411 | ! |
- ans <- FALSE+ datasets, |
| 303 | -+ | ||
| 412 | +! |
- }+ function(x) {
|
|
| 304 | -+ | ||
| 413 | +! |
-
+ var_names <- gsub( |
|
| 305 | +414 | ! |
- book1_values <- readRDS(file.path("shiny_bookmarks", book1, "values.rds"))
+ pattern = "\\s", |
| 306 | +415 | ! |
- book2_values <- readRDS(file.path("shiny_bookmarks", book2, "values.rds"))
+ replacement = "", |
| 307 | -+ | ||
| 416 | +! |
-
+ self$get_text( |
|
| 308 | +417 | ! |
- if (!isTRUE(all.equal(book1_values, book2_values))) {
+ sprintf( |
| 309 | +418 | ! |
- message("different values detected")
+ "#%s-filters-%s .filter-card-varname", |
| 310 | +419 | ! |
- message("choices for numeric filters MAY be different, see RangeFilterState$set_choices")
+ self$active_filters_ns(), |
| 311 | +420 | ! |
- ans <- FALSE+ x |
| 312 | +421 |
- }+ ) |
|
| 313 | +422 |
-
+ ) |
|
| 314 | -! | +||
| 423 | +
- if (ans) message("perfect!")
+ ) |
||
| 315 | +424 | ! |
- invisible(NULL)+ structure( |
| 316 | -+ | ||
| 425 | +! |
- }+ lapply(var_names, private$get_active_filter_selection, dataset_name = x), |
|
| 317 | -+ | ||
| 426 | +! |
-
+ names = var_names |
|
| 318 | +427 |
-
+ ) |
|
| 319 | +428 |
- # Replacement for [base::rapply] which doesn't handle NULL values - skips the evaluation+ } |
|
| 320 | +429 |
- # of the function and returns NULL for given element.+ ) |
|
| 321 | -+ | ||
| 430 | +! |
- rapply2 <- function(x, f) {
+ names(active_filters) <- datasets |
|
| 322 | -199x | +||
| 431 | +! |
- if (inherits(x, "list")) {
+ if (is.null(dataset_name)) {
|
|
| 323 | -87x | +||
| 432 | +! |
- lapply(x, rapply2, f = f)+ return(active_filters) |
|
| 324 | +433 |
- } else {
+ } |
|
| 325 | -112x | +||
| 434 | +! |
- f(x)+ active_filters[[dataset_name]] |
|
| 326 | +435 |
- }+ }, |
|
| 327 | +436 |
- }+ #' @description |
| 1 | +437 |
- #' Execute and validate `teal_data_module`+ #' Add a new variable from the dataset to be filtered. |
|
| 2 | +438 |
- #'+ #' |
|
| 3 | +439 |
- #' This is a low level module to handle `teal_data_module` execution and validation.+ #' @param dataset_name (character) The name of the dataset to add the filter variable to. |
|
| 4 | +440 |
- #' [teal_transform_module()] inherits from [teal_data_module()] so it is handled by this module too.+ #' @param var_name (character) The name of the variable to add to the filter panel. |
|
| 5 | +441 |
- #' [srv_teal()] accepts various `data` objects and eventually they are all transformed to `reactive`+ #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$set_inputs` |
|
| 6 | +442 |
- #' [teal.data::teal_data()] which is a standard data class in whole `teal` framework.+ #' |
|
| 7 | +443 |
- #'+ #' @return The `TealAppDriver` object invisibly. |
|
| 8 | +444 |
- #' @section data validation:+ add_filter_var = function(dataset_name, var_name, ...) {
|
|
| 9 | -+ | ||
| 445 | +! |
- #'+ checkmate::check_string(dataset_name) |
|
| 10 | -+ | ||
| 446 | +! |
- #' Executed [teal_data_module()] is validated and output is validated for consistency.+ checkmate::check_string(var_name) |
|
| 11 | -+ | ||
| 447 | +! |
- #' Output `data` is invalid if:+ private$set_active_ns() |
|
| 12 | -+ | ||
| 448 | +! |
- #' 1. [teal_data_module()] is invalid if server doesn't return `reactive`. **Immediately crashes an app!**+ self$click( |
|
| 13 | -+ | ||
| 449 | +! |
- #' 2. `reactive` throws a `shiny.error` - happens when module creating [teal.data::teal_data()] fails.+ selector = sprintf( |
|
| 14 | -+ | ||
| 450 | +! |
- #' 3. `reactive` returns `qenv.error` - happens when [teal.data::teal_data()] evaluates a failing code.+ "#%s-filters-%s-add_filter_icon", |
|
| 15 | -+ | ||
| 451 | +! |
- #' 4. `reactive` object doesn't return [teal.data::teal_data()].+ private$ns$filter_panel, |
|
| 16 | -+ | ||
| 452 | +! |
- #' 5. [teal.data::teal_data()] object lacks any `datanames` specified in the `modules` argument.+ dataset_name |
|
| 17 | +453 |
- #'+ ) |
|
| 18 | +454 |
- #' `teal` (observers in `srv_teal`) always waits to render an app until `reactive` `teal_data` is+ ) |
|
| 19 | -+ | ||
| 455 | +! |
- #' returned. If error 2-4 occurs, relevant error message is displayed to the app user. Once the issue is+ self$set_input( |
|
| 20 | -+ | ||
| 456 | +! |
- #' resolved, the app will continue to run. `teal` guarantees that errors in data don't crash the app+ sprintf( |
|
| 21 | -+ | ||
| 457 | +! |
- #' (except error 1).+ "%s-filters-%s-%s-filter-var_to_add", |
|
| 22 | -+ | ||
| 458 | +! |
- #'+ private$ns$filter_panel, |
|
| 23 | -+ | ||
| 459 | +! |
- #' @param id (`character(1)`) Module id+ dataset_name, |
|
| 24 | -+ | ||
| 460 | +! |
- #' @param data (`reactive teal_data`)+ dataset_name |
|
| 25 | +461 |
- #' @param data_module (`teal_data_module`)+ ), |
|
| 26 | -+ | ||
| 462 | +! |
- #' @param modules (`teal_modules` or `teal_module`) For `datanames` validation purpose+ var_name, |
|
| 27 | +463 |
- #' @param validate_shiny_silent_error (`logical`) If `TRUE`, then `shiny.silent.error` is validated and+ ... |
|
| 28 | +464 |
- #' @param is_transform_failed (`reactiveValues`) contains `logical` flags named after each transformator.+ ) |
|
| 29 | -+ | ||
| 465 | +! |
- #' Help to determine if any previous transformator failed, so that following transformators can be disabled+ invisible(self) |
|
| 30 | +466 |
- #' and display a generic failure message.+ }, |
|
| 31 | +467 |
- #'+ #' @description |
|
| 32 | +468 |
- #' @return `reactive` `teal_data`+ #' Remove an active filter variable of a dataset from the active filter variables panel. |
|
| 33 | +469 |
- #'+ #' |
|
| 34 | +470 |
- #' @rdname module_teal_data+ #' @param dataset_name (character) The name of the dataset to remove the filter variable from. |
|
| 35 | +471 |
- #' @name module_teal_data+ #' If `NULL`, all the filter variables will be removed. |
|
| 36 | +472 |
- #' @keywords internal+ #' @param var_name (character) The name of the variable to remove from the filter panel. |
|
| 37 | +473 |
- NULL+ #' If `NULL`, all the filter variables of the dataset will be removed. |
|
| 38 | +474 |
-
+ #' |
|
| 39 | +475 |
- #' @rdname module_teal_data+ #' @return The `TealAppDriver` object invisibly. |
|
| 40 | +476 |
- ui_teal_data <- function(id, data_module = function(id) NULL) {
+ remove_filter_var = function(dataset_name = NULL, var_name = NULL) {
|
|
| 41 | +477 | ! |
- checkmate::assert_string(id)+ checkmate::check_string(dataset_name, null.ok = TRUE) |
| 42 | +478 | ! |
- checkmate::assert_function(data_module, args = "id")+ checkmate::check_string(var_name, null.ok = TRUE) |
| 43 | +479 | ! |
- ns <- NS(id)- |
-
| 44 | -- |
-
+ if (is.null(dataset_name)) {
|
|
| 45 | +480 | ! |
- shiny::tagList(+ remove_selector <- sprintf( |
| 46 | +481 | ! |
- tags$div(id = ns("wrapper"), data_module(id = ns("data"))),
+ "#%s-active-remove_all_filters", |
| 47 | +482 | ! |
- ui_validate_reactive_teal_data(ns("validate"))
- |
-
| 48 | -- |
- )+ self$active_filters_ns() |
|
| 49 | +483 |
- }+ ) |
|
| 50 | -+ | ||
| 484 | +! |
-
+ } else if (is.null(var_name)) {
|
|
| 51 | -+ | ||
| 485 | +! |
- #' @rdname module_teal_data+ remove_selector <- sprintf( |
|
| 52 | -+ | ||
| 486 | +! |
- srv_teal_data <- function(id,+ "#%s-active-%s-remove_filters", |
|
| 53 | -+ | ||
| 487 | +! |
- data_module = function(id) NULL,+ self$active_filters_ns(), |
|
| 54 | -+ | ||
| 488 | +! |
- modules = NULL,+ dataset_name |
|
| 55 | +489 |
- validate_shiny_silent_error = TRUE,+ ) |
|
| 56 | +490 |
- is_transform_failed = reactiveValues()) {
- |
- |
| 57 | -! | -
- checkmate::assert_string(id)- |
- |
| 58 | -! | -
- checkmate::assert_function(data_module, args = "id")+ } else {
|
|
| 59 | +491 | ! |
- checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"), null.ok = TRUE)
+ remove_selector <- sprintf( |
| 60 | +492 | ! |
- checkmate::assert_class(is_transform_failed, "reactivevalues")- |
-
| 61 | -- |
-
+ "#%s-active-%s-filter-%s_%s-remove", |
|
| 62 | +493 | ! |
- moduleServer(id, function(input, output, session) {
+ self$active_filters_ns(), |
| 63 | +494 | ! |
- logger::log_debug("srv_teal_data initializing.")
+ dataset_name, |
| 64 | +495 | ! |
- is_transform_failed[[id]] <- FALSE+ dataset_name, |
| 65 | +496 | ! |
- data_out <- data_module(id = "data")+ var_name |
| 66 | -! | +||
| 497 | +
- data_handled <- reactive(tryCatch(data_out(), error = function(e) e))+ ) |
||
| 67 | -! | +||
| 498 | +
- observeEvent(data_handled(), {
+ } |
||
| 68 | +499 | ! |
- if (!inherits(data_handled(), "teal_data")) {
+ self$click( |
| 69 | +500 | ! |
- is_transform_failed[[id]] <- TRUE+ selector = remove_selector |
| 70 | +501 |
- } else {
+ ) |
|
| 71 | +502 | ! |
- is_transform_failed[[id]] <- FALSE+ invisible(self) |
| 72 | +503 |
- }+ }, |
|
| 73 | +504 |
- })+ #' @description |
|
| 74 | +505 |
-
+ #' Set the active filter values for a variable of a dataset in the active filter variable panel. |
|
| 75 | -! | +||
| 506 | +
- is_previous_failed <- reactive({
+ #' |
||
| 76 | -! | +||
| 507 | +
- idx_this <- which(names(is_transform_failed) == id)+ #' @param dataset_name (character) The name of the dataset to set the filter value for. |
||
| 77 | -! | +||
| 508 | +
- is_transform_failed_list <- reactiveValuesToList(is_transform_failed)+ #' @param var_name (character) The name of the variable to set the filter value for. |
||
| 78 | -! | +||
| 509 | +
- idx_failures <- which(unlist(is_transform_failed_list))+ #' @param input The value to set the filter to. |
||
| 79 | -! | +||
| 510 | +
- any(idx_failures < idx_this)+ #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$set_inputs` |
||
| 80 | +511 |
- })+ #' |
|
| 81 | +512 |
-
+ #' @return The `TealAppDriver` object invisibly. |
|
| 82 | -! | +||
| 513 | +
- observeEvent(is_previous_failed(), {
+ set_active_filter_selection = function(dataset_name, |
||
| 83 | -! | +||
| 514 | +
- if (is_previous_failed()) {
+ var_name, |
||
| 84 | -! | +||
| 515 | +
- shinyjs::disable("wrapper")
+ input, |
||
| 85 | +516 |
- } else {
+ ...) {
|
|
| 86 | +517 | ! |
- shinyjs::enable("wrapper")
+ checkmate::check_string(dataset_name) |
| 87 | -+ | ||
| 518 | +! |
- }+ checkmate::check_string(var_name) |
|
| 88 | -+ | ||
| 519 | +! |
- })+ checkmate::check_string(input) |
|
| 89 | +520 | ||
| 90 | +521 | ! |
- srv_validate_reactive_teal_data(+ input_id_prefix <- sprintf( |
| 91 | +522 | ! |
- "validate",+ "%s-filters-%s-filter-%s_%s-inputs", |
| 92 | +523 | ! |
- data = data_handled,+ self$active_filters_ns(), |
| 93 | +524 | ! |
- modules = modules,+ dataset_name, |
| 94 | +525 | ! |
- validate_shiny_silent_error = validate_shiny_silent_error,+ dataset_name, |
| 95 | +526 | ! |
- hide_validation_error = is_previous_failed- |
-
| 96 | -- |
- )- |
- |
| 97 | -- |
- })+ var_name |
|
| 98 | +527 |
- }+ ) |
|
| 99 | +528 | ||
| 100 | -- |
- #' @rdname module_teal_data- |
- |
| 101 | +529 |
- ui_validate_reactive_teal_data <- function(id) {
+ # Find the type of filter (based on filter panel) |
|
| 102 | +530 | ! |
- ns <- NS(id)+ supported_suffix <- c("selection", "selection_manual")
|
| 103 | +531 | ! |
- tagList(+ slices_suffix <- supported_suffix[ |
| 104 | +532 | ! |
- div(+ match( |
| 105 | +533 | ! |
- id = ns("validate_messages"),
+ TRUE, |
| 106 | +534 | ! |
- class = "teal_validated",+ vapply( |
| 107 | +535 | ! |
- ui_validate_error(ns("silent_error")),
+ supported_suffix, |
| 108 | +536 | ! |
- ui_check_class_teal_data(ns("class_teal_data")),
+ function(suffix) {
|
| 109 | +537 | ! |
- ui_check_module_datanames(ns("shiny_warnings"))
+ !is.null(self$get_html(sprintf("#%s-%s", input_id_prefix, suffix)))
|
| 110 | +538 |
- ),- |
- |
| 111 | -! | -
- div(- |
- |
| 112 | -! | -
- class = "teal_validated",+ }, |
|
| 113 | +539 | ! |
- uiOutput(ns("previous_failed"))
+ logical(1) |
| 114 | +540 |
- )+ ) |
|
| 115 | +541 |
- )+ ) |
|
| 116 | +542 |
- }+ ] |
|
| 117 | +543 | ||
| 118 | +544 |
- #' @rdname module_teal_data+ # Generate correct namespace |
|
| 119 | -+ | ||
| 545 | +! |
- srv_validate_reactive_teal_data <- function(id, # nolint: object_length+ slices_input_id <- sprintf( |
|
| 120 | -+ | ||
| 546 | +! |
- data,+ "%s-filters-%s-filter-%s_%s-inputs-%s", |
|
| 121 | -+ | ||
| 547 | +! |
- modules = NULL,+ self$active_filters_ns(), |
|
| 122 | -+ | ||
| 548 | +! |
- validate_shiny_silent_error = FALSE,+ dataset_name, |
|
| 123 | -+ | ||
| 549 | +! |
- hide_validation_error = reactive(FALSE)) {
+ dataset_name, |
|
| 124 | +550 | ! |
- checkmate::assert_string(id)+ var_name, |
| 125 | +551 | ! |
- checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"), null.ok = TRUE)
+ slices_suffix |
| 126 | -! | +||
| 552 | +
- checkmate::assert_flag(validate_shiny_silent_error)+ ) |
||
| 127 | +553 | ||
| 128 | +554 | ! |
- moduleServer(id, function(input, output, session) {
+ if (identical(slices_suffix, "selection_manual")) {
+ |
+
| 555 | +! | +
+ checkmate::assert_numeric(input, len = 2) |
|
| 129 | +556 |
- # there is an empty reactive cycle on `init` and `data_rv` has `shiny.silent.error` class+ |
|
| 130 | +557 | ! |
- srv_validate_error("silent_error", data, validate_shiny_silent_error)
+ dots <- rlang::list2(...) |
| 131 | +558 | ! |
- srv_check_class_teal_data("class_teal_data", data)
+ checkmate::assert_choice(dots$priority_, formals(self$set_inputs)[["priority_"]], null.ok = TRUE) |
| 132 | +559 | ! |
- srv_check_module_datanames("shiny_warnings", data, modules)
+ checkmate::assert_flag(dots$wait_, null.ok = TRUE)+ |
+
| 560 | ++ | + | |
| 133 | +561 | ! |
- output$previous_failed <- renderUI({
+ self$run_js( |
| 134 | +562 | ! |
- if (hide_validation_error()) {
+ sprintf( |
| 135 | +563 | ! |
- shinyjs::hide("validate_messages")
+ "Shiny.setInputValue('%s:sw.numericRange', [%f, %f], {priority: '%s'})",
|
| 136 | +564 | ! |
- tags$div("One of previous transformators failed. Please check its inputs.", class = "teal-output-warning")
+ slices_input_id, |
| 137 | -+ | ||
| 565 | +! |
- } else {
+ input[[1]], |
|
| 138 | +566 | ! |
- shinyjs::show("validate_messages")
+ input[[2]], |
| 139 | +567 | ! |
- NULL+ priority_ = ifelse(is.null(dots$priority_), "input", dots$priority_) |
| 140 | +568 |
- }+ ) |
|
| 141 | +569 |
- })+ ) |
|
| 142 | +570 | ||
| 143 | +571 | ! |
- .trigger_on_success(data)+ if (isTRUE(dots$wait_) || is.null(dots$wait_)) {
|
| 144 | -+ | ||
| 572 | +! |
- })+ self$wait_for_idle( |
|
| 145 | -+ | ||
| 573 | +! |
- }+ timeout = if (is.null(dots$timeout_)) rlang::missing_arg() else dots$timeout_ |
|
| 146 | +574 |
-
+ ) |
|
| 147 | +575 |
- #' @keywords internal+ } |
|
| 148 | -+ | ||
| 576 | +! |
- ui_validate_error <- function(id) {
+ } else if (identical(slices_suffix, "selection")) {
|
|
| 149 | -116x | +||
| 577 | +! |
- ns <- NS(id)+ self$set_input( |
|
| 150 | -116x | +||
| 578 | +! |
- uiOutput(ns("message"))
+ slices_input_id,+ |
+ |
| 579 | +! | +
+ input, |
|
| 151 | +580 |
- }+ ... |
|
| 152 | +581 |
-
+ ) |
|
| 153 | +582 |
- #' @keywords internal+ } else {
+ |
+ |
| 583 | +! | +
+ stop("Filter selection set not supported for this slice.")
|
|
| 154 | +584 |
- srv_validate_error <- function(id, data, validate_shiny_silent_error) {
+ } |
|
| 155 | -113x | +||
| 585 | +
- checkmate::assert_string(id)+ |
||
| 156 | -113x | +||
| 586 | +! |
- checkmate::assert_flag(validate_shiny_silent_error)+ invisible(self) |
|
| 157 | -113x | +||
| 587 | +
- moduleServer(id, function(input, output, session) {
+ }, |
||
| 158 | -113x | +||
| 588 | +
- output$message <- renderUI({
+ #' @description |
||
| 159 | -112x | +||
| 589 | +
- is_shiny_silent_error <- inherits(data(), "shiny.silent.error") && identical(data()$message, "")+ #' Extract `html` attribute (found by a `selector`). |
||
| 160 | -112x | +||
| 590 | +
- if (inherits(data(), "qenv.error")) {
+ #' |
||
| 161 | -2x | +||
| 591 | +
- validate(+ #' @param selector (`character(1)`) specifying the selector to be used to get the content of a specific node. |
||
| 162 | -2x | +||
| 592 | +
- need(+ #' @param attribute (`character(1)`) name of an attribute to retrieve from a node specified by `selector`. |
||
| 163 | -2x | +||
| 593 | +
- FALSE,+ #' |
||
| 164 | -2x | +||
| 594 | +
- paste(+ #' @return The `character` vector. |
||
| 165 | -2x | +||
| 595 | +
- "Error when executing the `data` module:",+ get_attr = function(selector, attribute) {
|
||
| 166 | -2x | +||
| 596 | +! |
- strip_style(paste(data()$message, collapse = "\n")),+ rvest::html_attr( |
|
| 167 | -2x | +||
| 597 | +! |
- "\nCheck your inputs or contact app developer if error persists.",+ rvest::html_nodes(self$get_html_rvest("html"), selector),
|
|
| 168 | -2x | +||
| 598 | +! |
- collapse = "\n"+ attribute |
|
| 169 | +599 |
- )+ ) |
|
| 170 | +600 |
- )+ }, |
|
| 171 | +601 |
- )+ #' @description |
|
| 172 | -110x | +||
| 602 | +
- } else if (inherits(data(), "error")) {
+ #' Wrapper around `get_html` that passes the output directly to `rvest::read_html`. |
||
| 173 | -11x | +||
| 603 | +
- if (is_shiny_silent_error && !validate_shiny_silent_error) {
+ #' |
||
| 174 | -4x | +||
| 604 | +
- return(NULL)+ #' @param selector `(character(1))` passed to `get_html`. |
||
| 175 | +605 |
- }+ #' |
|
| 176 | -7x | +||
| 606 | +
- validate(+ #' @return An XML document. |
||
| 177 | -7x | +||
| 607 | +
- need(+ get_html_rvest = function(selector) {
|
||
| 178 | -7x | +||
| 608 | +! |
- FALSE,+ rvest::read_html(self$get_html(selector)) |
|
| 179 | -7x | +||
| 609 | +
- sprintf(+ }, |
||
| 180 | -7x | +||
| 610 | +
- "Shiny error when executing the `data` module.\n%s\n%s",+ #' Wrapper around `get_url()` method that opens the app in the browser. |
||
| 181 | -7x | +||
| 611 | +
- data()$message,+ #' |
||
| 182 | -7x | +||
| 612 | +
- "Check your inputs or contact app developer if error persists."+ #' @return Nothing. Opens the underlying teal app in the browser. |
||
| 183 | +613 |
- )+ open_url = function() {
|
|
| 184 | -+ | ||
| 614 | +! |
- )+ browseURL(self$get_url()) |
|
| 185 | +615 |
- )+ }, |
|
| 186 | +616 |
- }+ #' @description |
|
| 187 | +617 |
- })+ #' Waits until a specified input, output, or export value. |
|
| 188 | +618 |
- })+ #' This function serves as a wrapper around the `wait_for_value` method, |
|
| 189 | +619 |
- }+ #' providing a more flexible interface for waiting on different types of values within the active module namespace. |
|
| 190 | +620 |
-
+ #' @param input,output,export A name of an input, output, or export value. |
|
| 191 | +621 |
-
+ #' Only one of these parameters may be used. |
|
| 192 | +622 |
- #' @keywords internal+ #' @param ... Must be empty. Allows for parameter expansion. |
|
| 193 | +623 |
- ui_check_class_teal_data <- function(id) {
+ #' Parameter with additional value to passed in `wait_for_value`. |
|
| 194 | -116x | +||
| 624 | +
- ns <- NS(id)+ wait_for_active_module_value = function(input = rlang::missing_arg(), |
||
| 195 | -116x | +||
| 625 | +
- uiOutput(ns("message"))
+ output = rlang::missing_arg(), |
||
| 196 | +626 |
- }+ export = rlang::missing_arg(), |
|
| 197 | +627 |
-
+ ...) {
|
|
| 198 | -+ | ||
| 628 | +! |
- #' @keywords internal+ ns <- shiny::NS(self$active_module_ns()) |
|
| 199 | +629 |
- srv_check_class_teal_data <- function(id, data) {
+
|
|
| 200 | -113x | +||
| 630 | +! |
- checkmate::assert_string(id)+ if (!rlang::is_missing(input) && checkmate::test_string(input, min.chars = 1)) input <- ns(input) |
|
| 201 | -113x | +||
| 631 | +! |
- moduleServer(id, function(input, output, session) {
+ if (!rlang::is_missing(output) && checkmate::test_string(output, min.chars = 1)) output <- ns(output) |
|
| 202 | -113x | +||
| 632 | +! |
- output$message <- renderUI({
+ if (!rlang::is_missing(export) && checkmate::test_string(export, min.chars = 1)) export <- ns(export) |
|
| 203 | -112x | +||
| 633 | +
- validate(+ |
||
| 204 | -112x | +||
| 634 | +! |
- need(+ self$wait_for_value( |
|
| 205 | -112x | +||
| 635 | +! |
- inherits(data(), c("teal_data", "error")),
+ input = input, |
|
| 206 | -112x | +||
| 636 | +! |
- "Did not receive `teal_data` object. Cannot proceed further."+ output = output, |
|
| 207 | -+ | ||
| 637 | +! |
- )+ export = export, |
|
| 208 | +638 |
- )+ ... |
|
| 209 | +639 |
- })+ ) |
|
| 210 | +640 |
- })+ } |
|
| 211 | +641 |
- }+ ), |
|
| 212 | +642 |
-
+ # private members ---- |
|
| 213 | +643 |
- #' @keywords internal+ private = list( |
|
| 214 | +644 |
- ui_check_module_datanames <- function(id) {
- |
- |
| 215 | -116x | -
- ns <- NS(id)+ # private attributes ---- |
|
| 216 | -116x | +||
| 645 | +
- uiOutput(NS(id, "message"))+ data = NULL, |
||
| 217 | +646 |
- }+ modules = NULL, |
|
| 218 | +647 |
-
+ filter = teal_slices(), |
|
| 219 | +648 |
- #' @keywords internal+ ns = list( |
|
| 220 | +649 |
- srv_check_module_datanames <- function(id, data, modules) {
+ module = character(0), |
|
| 221 | -193x | +||
| 650 | +
- checkmate::assert_string(id)+ filter_panel = character(0) |
||
| 222 | -193x | +||
| 651 | +
- moduleServer(id, function(input, output, session) {
+ ), |
||
| 223 | -193x | +||
| 652 | +
- output$message <- renderUI({
+ # private methods ---- |
||
| 224 | -196x | +||
| 653 | +
- if (inherits(data(), "teal_data")) {
+ set_active_ns = function() {
|
||
| 225 | -179x | +||
| 654 | +! |
- is_modules_ok <- check_modules_datanames_html(+ all_inputs <- self$get_values()$input |
|
| 226 | -179x | +||
| 655 | +! |
- modules = modules, datanames = names(data())+ active_tab_inputs <- all_inputs[grepl("-active_tab$", names(all_inputs))]
|
|
| 227 | +656 |
- )- |
- |
| 228 | -179x | -
- if (!isTRUE(is_modules_ok)) {
+
|
|
| 229 | -19x | +||
| 657 | +! |
- tags$div(is_modules_ok, class = "teal-output-warning")+ tab_ns <- unlist(lapply(names(active_tab_inputs), function(name) {
|
|
| 230 | -+ | ||
| 658 | +! |
- }+ gsub( |
|
| 231 | -+ | ||
| 659 | +! |
- }+ pattern = "-active_tab$", |
|
| 232 | -+ | ||
| 660 | +! |
- })+ replacement = sprintf("-%s", active_tab_inputs[[name]]),
|
|
| 233 | -+ | ||
| 661 | +! |
- })+ name |
|
| 234 | +662 |
- }+ ) |
|
| 235 | +663 |
-
+ })) |
|
| 236 | -+ | ||
| 664 | +! |
- .trigger_on_success <- function(data) {
+ active_ns <- tab_ns[1] |
|
| 237 | -113x | +||
| 665 | +! |
- out <- reactiveVal(NULL)+ if (length(tab_ns) > 1) {
|
|
| 238 | -113x | +||
| 666 | +! |
- observeEvent(data(), {
+ for (i in 2:length(tab_ns)) {
|
- |
| 239 | -112x | +||
| 667 | +! |
- if (inherits(data(), "teal_data")) {
+ next_ns <- tab_ns[i] |
|
| 240 | -97x | +||
| 668 | +! |
- if (!identical(data(), out())) {
+ if (grepl(pattern = active_ns, next_ns)) {
|
|
| 241 | -97x | +||
| 669 | +! |
- out(data())+ active_ns <- next_ns |
|
| 242 | +670 |
- }+ } |
|
| 243 | +671 |
- }+ } |
|
| 244 | +672 |
- })+ }+ |
+ |
| 673 | +! | +
+ private$ns$module <- sprintf("%s-%s", active_ns, "module")
|
|
| 245 | +674 | ||
| 246 | -113x | +||
| 675 | +! |
- out+ components <- c("filter_panel", "data_summary")
|
|
| 247 | -+ | ||
| 676 | +! |
- }+ for (component in components) {
|
| 1 | +677 |
- #' Module to transform `reactive` `teal_data`+ if ( |
|
| 2 | -+ | ||
| 678 | +! |
- #'+ !is.null(self$get_html(sprintf("#%s-%s-panel", active_ns, component))) ||
|
|
| 3 | -+ | ||
| 679 | +! |
- #' Module calls [teal_transform_module()] in sequence so that `reactive teal_data` output+ !is.null(self$get_html(sprintf("#%s-%s-table", active_ns, component)))
|
|
| 4 | +680 |
- #' from one module is handed over to the following module's input.+ ) {
|
|
| 5 | -+ | ||
| 681 | +! |
- #'+ private$ns[[component]] <- sprintf("%s-%s", active_ns, component)
|
|
| 6 | +682 |
- #' @inheritParams module_teal_data+ } else {
+ |
+ |
| 683 | +! | +
+ private$ns[[component]] <- sprintf("%s-module_%s", active_ns, component)
|
|
| 7 | +684 |
- #' @inheritParams teal_modules+ } |
|
| 8 | +685 |
- #' @param class (character(1)) CSS class to be added in the `div` wrapper tag.+ } |
|
| 9 | +686 |
-
+ }, |
|
| 10 | +687 |
- #' @return `reactive` `teal_data`+ # @description |
|
| 11 | +688 |
- #'+ # Get the active filter values from the active filter selection of dataset from the filter panel. |
|
| 12 | +689 |
- #' @name module_transform_data+ # |
|
| 13 | +690 |
- NULL+ # @param dataset_name (character) The name of the dataset to get the filter values from. |
|
| 14 | +691 |
-
+ # @param var_name (character) The name of the variable to get the filter values from. |
|
| 15 | +692 |
- #' @export+ # |
|
| 16 | +693 |
- #' @rdname module_transform_data+ # @return The value of the active filter selection. |
|
| 17 | +694 |
- ui_transform_teal_data <- function(id, transformators, class = "well") {
+ get_active_filter_selection = function(dataset_name, var_name) {
|
|
| 18 | -1x | +||
| 695 | +! |
- checkmate::assert_string(id)+ checkmate::check_string(dataset_name) |
|
| 19 | -1x | +||
| 696 | +! |
- if (length(transformators) == 0L) {
+ checkmate::check_string(var_name) |
|
| 20 | +697 | ! |
- return(NULL)+ input_id_prefix <- sprintf( |
| 21 | -+ | ||
| 698 | +! |
- }+ "%s-filters-%s-filter-%s_%s-inputs", |
|
| 22 | -1x | +||
| 699 | +! |
- if (inherits(transformators, "teal_transform_module")) {
+ self$active_filters_ns(), |
|
| 23 | -1x | +||
| 700 | +! |
- transformators <- list(transformators)+ dataset_name, |
|
| 24 | -+ | ||
| 701 | +! |
- }+ dataset_name, |
|
| 25 | -1x | +||
| 702 | +! |
- checkmate::assert_list(transformators, "teal_transform_module")+ var_name |
|
| 26 | -1x | +||
| 703 | +
- names(transformators) <- sprintf("transform_%d", seq_len(length(transformators)))
+ ) |
||
| 27 | +704 | ||
| 28 | -1x | +||
| 705 | +
- lapply(+ # Find the type of filter (categorical or range) |
||
| 29 | -1x | +||
| 706 | +! |
- names(transformators),+ supported_suffix <- c("selection", "selection_manual")
|
|
| 30 | -1x | +||
| 707 | +! |
- function(name) {
+ for (suffix in supported_suffix) {
|
|
| 31 | -1x | +||
| 708 | +! |
- child_id <- NS(id, name)+ if (!is.null(self$get_html(sprintf("#%s-%s", input_id_prefix, suffix)))) {
|
|
| 32 | -1x | +||
| 709 | +! |
- ns <- NS(child_id)+ return(self$get_value(input = sprintf("%s-%s", input_id_prefix, suffix)))
|
|
| 33 | -1x | +||
| 710 | +
- data_mod <- transformators[[name]]+ } |
||
| 34 | -1x | +||
| 711 | +
- transform_wrapper_id <- ns(sprintf("wrapper_%s", name))
+ } |
||
| 35 | +712 | ||
| 36 | -1x | +||
| 713 | +! |
- display_fun <- if (is.null(data_mod$ui)) shinyjs::hidden else function(x) x+ NULL # If there are not any supported filters |
|
| 37 | +714 | - - | -|
| 38 | -1x | -
- display_fun(+ }, |
|
| 39 | -1x | +||
| 715 | +
- div(+ # @description |
||
| 40 | +716 |
- # class .teal_validated changes the color of the boarder on error in ui_validate_reactive_teal_data+ # Check if the page is stable without any `DOM` updates in the body of the app. |
|
| 41 | +717 |
- # For details see tealValidate.js file.+ # This is achieved by blocing the R process by sleeping until the page is unchanged till the `stability_period`. |
|
| 42 | -1x | +||
| 718 | +
- id = ns("wrapper"),
+ # @param stability_period (`numeric(1)`) The time in milliseconds to wait till the page to be stable. |
||
| 43 | -1x | +||
| 719 | +
- class = c(class, "teal_validated"),+ # @param check_interval (`numeric(1)`) The time in milliseconds to check for changes in the page. |
||
| 44 | -1x | +||
| 720 | +
- title = attr(data_mod, "label"),+ # The stability check is reset when a change is detected in the page after sleeping for check_interval. |
||
| 45 | -1x | +||
| 721 | +
- tags$span(+ wait_for_page_stability = function(stability_period = 2000, check_interval = 200) {
|
||
| 46 | -1x | +||
| 722 | +! |
- class = "text-primary mb-4",+ previous_content <- self$get_html("body")
|
|
| 47 | -1x | +||
| 723 | +! |
- icon("fas fa-square-pen"),
+ end_time <- Sys.time() + (stability_period / 1000) |
|
| 48 | -1x | +||
| 724 | +
- attr(data_mod, "label")+ |
||
| 49 | -+ | ||
| 725 | +! |
- ),+ repeat {
|
|
| 50 | -1x | +||
| 726 | +! |
- tags$i(+ Sys.sleep(check_interval / 1000) |
|
| 51 | -1x | +||
| 727 | +! |
- class = "remove pull-right fa fa-angle-down",+ current_content <- self$get_html("body")
|
|
| 52 | -1x | +||
| 728 | +
- style = "cursor: pointer;",+ |
||
| 53 | -1x | +||
| 729 | +! |
- title = "fold/expand transformator panel",+ if (!identical(previous_content, current_content)) {
|
|
| 54 | -1x | +||
| 730 | +! |
- onclick = sprintf("togglePanelItems(this, '%s', 'fa-angle-right', 'fa-angle-down');", transform_wrapper_id)
+ previous_content <- current_content |
|
| 55 | -+ | ||
| 731 | +! |
- ),+ end_time <- Sys.time() + (stability_period / 1000) |
|
| 56 | -1x | +||
| 732 | +! |
- tags$div(+ } else if (Sys.time() >= end_time) {
|
|
| 57 | -1x | +||
| 733 | +! |
- id = transform_wrapper_id,+ break |
|
| 58 | -1x | +||
| 734 | +
- if (is.null(data_mod$ui)) {
+ } |
||
| 59 | -! | +||
| 735 | +
- return(NULL)+ } |
||
| 60 | +736 |
- } else {
+ } |
|
| 61 | -1x | +||
| 737 | +
- data_mod$ui(id = ns("transform"))
+ ) |
||
| 62 | +738 |
- },+ ) |
|
| 63 | -1x | +
| 1 | +
- div(+ #' Landing popup module |
||
| 64 | -1x | +||
| 2 | +
- id = ns("validate_messages"),
+ #' |
||
| 65 | -1x | +||
| 3 | +
- class = "teal_validated",+ #' @description Creates a landing welcome popup for `teal` applications. |
||
| 66 | -1x | +||
| 4 | +
- uiOutput(ns("error_wrapper"))
+ #' |
||
| 67 | +5 |
- )+ #' This module is used to display a popup dialog when the application starts. |
|
| 68 | +6 |
- )+ #' The dialog blocks access to the application and must be closed with a button before the application can be viewed. |
|
| 69 | +7 |
- )+ #' |
|
| 70 | +8 |
- )+ #' @param label (`character(1)`) Label of the module. |
|
| 71 | +9 |
- }+ #' @param title (`character(1)`) Text to be displayed as popup title. |
|
| 72 | +10 |
- )+ #' @param content (`character(1)`, `shiny.tag` or `shiny.tag.list`) with the content of the popup. |
|
| 73 | +11 |
- }+ #' Passed to `...` of `shiny::modalDialog`. See examples. |
|
| 74 | +12 |
-
+ #' @param buttons (`shiny.tag` or `shiny.tag.list`) Typically a `modalButton` or `actionButton`. See examples. |
|
| 75 | +13 |
- #' @export+ #' |
|
| 76 | +14 |
- #' @rdname module_transform_data+ #' @return A `teal_module` (extended with `teal_landing_module` class) to be used in `teal` applications. |
|
| 77 | +15 |
- srv_transform_teal_data <- function(id, data, transformators, modules = NULL, is_transform_failed = reactiveValues()) {
+ #' |
|
| 78 | -94x | +||
| 16 | +
- checkmate::assert_string(id)+ #' @examples |
||
| 79 | -94x | +||
| 17 | +
- assert_reactive(data)+ #' app1 <- init( |
||
| 80 | -94x | +||
| 18 | +
- checkmate::assert_class(modules, "teal_module", null.ok = TRUE)+ #' data = teal_data(iris = iris), |
||
| 81 | -94x | +||
| 19 | +
- if (length(transformators) == 0L) {
+ #' modules = modules( |
||
| 82 | -71x | +||
| 20 | +
- return(data)+ #' example_module() |
||
| 83 | +21 |
- }+ #' ), |
|
| 84 | -23x | +||
| 22 | +
- if (inherits(transformators, "teal_transform_module")) {
+ #' landing_popup = landing_popup_module( |
||
| 85 | -3x | +||
| 23 | +
- transformators <- list(transformators)+ #' content = "A place for the welcome message or a disclaimer statement.", |
||
| 86 | +24 |
- }+ #' buttons = modalButton("Proceed")
|
|
| 87 | -23x | +||
| 25 | +
- checkmate::assert_list(transformators, "teal_transform_module", null.ok = TRUE)+ #' ) |
||
| 88 | -23x | +||
| 26 | +
- names(transformators) <- sprintf("transform_%d", seq_len(length(transformators)))
+ #' ) |
||
| 89 | +27 |
-
+ #' if (interactive()) {
|
|
| 90 | -23x | +||
| 28 | +
- moduleServer(id, function(input, output, session) {
+ #' shinyApp(app1$ui, app1$server) |
||
| 91 | -23x | +||
| 29 | +
- module_output <- Reduce(+ #' } |
||
| 92 | -23x | +||
| 30 | +
- function(data_previous, name) {
+ #' |
||
| 93 | -26x | +||
| 31 | +
- moduleServer(name, function(input, output, session) {
+ #' app2 <- init( |
||
| 94 | -26x | +||
| 32 | +
- logger::log_debug("srv_transform_teal_data initializing for { name }.")
+ #' data = teal_data(iris = iris), |
||
| 95 | -26x | +||
| 33 | +
- is_transform_failed[[name]] <- FALSE+ #' modules = modules( |
||
| 96 | -26x | +||
| 34 | +
- data_out <- transformators[[name]]$server("transform", data = data_previous)
+ #' example_module() |
||
| 97 | -26x | +||
| 35 | +
- data_handled <- reactive(tryCatch(data_out(), error = function(e) e))+ #' ), |
||
| 98 | -26x | +||
| 36 | +
- observeEvent(data_handled(), {
+ #' landing_popup = landing_popup_module( |
||
| 99 | -32x | +||
| 37 | +
- if (inherits(data_handled(), "teal_data")) {
+ #' title = "Welcome", |
||
| 100 | -22x | +||
| 38 | +
- is_transform_failed[[name]] <- FALSE+ #' content = tags$b( |
||
| 101 | +39 |
- } else {
+ #' "A place for the welcome message or a disclaimer statement.", |
|
| 102 | -10x | +||
| 40 | +
- is_transform_failed[[name]] <- TRUE+ #' style = "color: red;" |
||
| 103 | +41 |
- }+ #' ), |
|
| 104 | +42 |
- })+ #' buttons = tagList( |
|
| 105 | +43 |
-
+ #' modalButton("Proceed"),
|
|
| 106 | -26x | +||
| 44 | +
- is_previous_failed <- reactive({
+ #' actionButton("read", "Read more",
|
||
| 107 | -29x | +||
| 45 | +
- idx_this <- which(names(is_transform_failed) == name)+ #' onclick = "window.open('http://google.com', '_blank')"
|
||
| 108 | -29x | +||
| 46 | +
- is_transform_failed_list <- reactiveValuesToList(is_transform_failed)+ #' ), |
||
| 109 | -29x | +||
| 47 | +
- idx_failures <- which(unlist(is_transform_failed_list))+ #' actionButton("close", "Reject", onclick = "window.close()")
|
||
| 110 | -29x | +||
| 48 | +
- any(idx_failures < idx_this)+ #' ) |
||
| 111 | +49 |
- })+ #' ) |
|
| 112 | +50 |
-
+ #' ) |
|
| 113 | -26x | +||
| 51 | +
- srv_validate_error("silent_error", data_handled, validate_shiny_silent_error = FALSE)
+ #' |
||
| 114 | -26x | +||
| 52 | +
- srv_check_class_teal_data("class_teal_data", data_handled)
+ #' if (interactive()) {
|
||
| 115 | -26x | +||
| 53 | +
- if (!is.null(modules)) {
+ #' shinyApp(app2$ui, app2$server) |
||
| 116 | -20x | +||
| 54 | +
- srv_check_module_datanames("datanames_warning", data_handled, modules)
+ #' } |
||
| 117 | +55 |
- }+ #' |
|
| 118 | +56 |
-
+ #' @export |
|
| 119 | +57 |
- # When there is no UI (`ui = NULL`) it should still show the errors+ landing_popup_module <- function(label = "Landing Popup", |
|
| 120 | -26x | +||
| 58 | +
- observe({
+ title = NULL, |
||
| 121 | -32x | +||
| 59 | +
- if (!inherits(data_handled(), "teal_data") && !is_previous_failed()) {
+ content = NULL, |
||
| 122 | -10x | +||
| 60 | +
- shinyjs::show("wrapper")
+ buttons = modalButton("Accept")) {
|
||
| 123 | -+ | ||
| 61 | +! |
- }+ checkmate::assert_string(label) |
|
| 124 | -+ | ||
| 62 | +! |
- })+ checkmate::assert_string(title, null.ok = TRUE) |
|
| 125 | -+ | ||
| 63 | +! |
-
+ checkmate::assert_multi_class( |
|
| 126 | -26x | +||
| 64 | +! |
- transform_wrapper_id <- sprintf("wrapper_%s", name)
+ content, |
|
| 127 | -26x | +||
| 65 | +! |
- output$error_wrapper <- renderUI({
+ classes = c("character", "shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE
|
|
| 128 | -29x | +||
| 66 | +
- if (is_previous_failed()) {
+ ) |
||
| 129 | +67 | ! |
- shinyjs::disable(transform_wrapper_id)+ checkmate::assert_multi_class(buttons, classes = c("shiny.tag", "shiny.tag.list"))
+ |
+
| 68 | ++ | + | |
| 130 | +69 | ! |
- tags$div("One of previous transformators failed. Please check its inputs.", class = "teal-output-warning")
+ message("Initializing landing_popup_module")
|
| 131 | +70 |
- } else {
+
|
|
| 132 | -29x | +||
| 71 | +! |
- shinyjs::enable(transform_wrapper_id)+ module <- module( |
|
| 133 | -29x | +||
| 72 | +! |
- shiny::tagList(+ label = label, |
|
| 134 | -29x | +||
| 73 | +! |
- ui_validate_error(session$ns("silent_error")),
+ server = function(id) {
|
|
| 135 | -29x | +||
| 74 | +! |
- ui_check_class_teal_data(session$ns("class_teal_data")),
+ moduleServer(id, function(input, output, session) {
|
|
| 136 | -29x | +||
| 75 | +! |
- ui_check_module_datanames(session$ns("datanames_warning"))
+ showModal( |
|
| 137 | -+ | ||
| 76 | +! |
- )+ modalDialog( |
|
| 138 | -+ | ||
| 77 | +! |
- }+ id = "landingpopup", |
|
| 139 | -+ | ||
| 78 | +! |
- })+ title = title, |
|
| 140 | -+ | ||
| 79 | +! |
-
+ content, |
|
| 141 | -26x | +||
| 80 | +! |
- .trigger_on_success(data_handled)+ footer = buttons |
|
| 142 | +81 |
- })+ ) |
|
| 143 | +82 |
- },+ ) |
|
| 144 | -23x | +||
| 83 | +
- x = names(transformators),+ }) |
||
| 145 | -23x | +||
| 84 | +
- init = data+ } |
||
| 146 | +85 |
- )+ ) |
|
| 147 | -23x | +||
| 86 | +! |
- module_output+ class(module) <- c("teal_module_landing", class(module))
|
|
| 148 | -+ | ||
| 87 | +! |
- })+ module |
|
| 149 | +88 |
}@@ -34843,14 +34229,14 @@ teal coverage - 60.11% |
| 1 |
- #' Evaluate expression on `teal_data_module`+ #' App state management. |
||
| 3 |
- #' @details+ #' @description |
||
| 4 |
- #' `within` is a convenience function for evaluating inline code inside the environment of a `teal_data_module`.+ #' `r lifecycle::badge("experimental")`
|
||
| 5 |
- #' It accepts only inline expressions (both simple and compound) and allows for injecting values into `expr` through+ #' |
||
| 6 |
- #' the `...` argument: as `name:value` pairs are passed to `...`, `name` in `expr` will be replaced with `value.`+ #' Capture and restore the global (app) input state. |
||
| 8 |
- #' @param data (`teal_data_module`) object+ #' @details |
||
| 9 |
- #' @param expr (`expression`) to evaluate. Must be inline code. See [within()]+ #' This module introduces bookmarks into `teal` apps: the `shiny` bookmarking mechanism becomes enabled |
||
| 10 |
- #' @param ... See `Details`.+ #' and server-side bookmarks can be created. |
||
| 12 |
- #' @return+ #' The bookmark manager presents a button with the bookmark icon and is placed in the tab-bar. |
||
| 13 |
- #' `within` returns a `teal_data_module` object with a delayed evaluation of `expr` when the module is run.+ #' When clicked, the button creates a bookmark and opens a modal which displays the bookmark URL. |
||
| 15 |
- #' @examples+ #' `teal` does not guarantee that all modules (`teal_module` objects) are bookmarkable. |
||
| 16 |
- #' within(tdm, dataset1 <- subset(dataset1, Species == "virginica"))+ #' 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 |
- #' # use additional parameter for expression value substitution.+ #' In order to communicate that a external module is bookmarkable, the module developer |
||
| 19 |
- #' valid_species <- "versicolor"+ #' should set the `teal_bookmarkable` attribute to `TRUE`. |
||
| 20 |
- #' within(tdm, dataset1 <- subset(dataset1, Species %in% species), species = valid_species)+ #' |
||
| 21 |
- #' @include teal_data_module.R+ #' @section Server logic: |
||
| 22 |
- #' @name within+ #' A bookmark is a URL that contains the app address with a `/?_state_id_=<bookmark_dir>` suffix. |
||
| 23 |
- #' @rdname teal_data_module+ #' `<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 |
- #' @export+ #' |
||
| 26 |
- #'+ #' @section Note: |
||
| 27 |
- within.teal_data_module <- function(data, expr, ...) {
+ #' To enable bookmarking use either: |
||
| 28 | -2x | +
- expr <- substitute(expr)+ #' - `shiny` app by using `shinyApp(..., enableBookmarking = "server")` (not supported in `shinytest2`) |
|
| 29 | -2x | +
- extras <- list(...)+ #' - set `options(shiny.bookmarkStore = "server")` before running the app |
|
| 30 |
-
+ #' |
||
| 31 |
- # Add braces for consistency.+ #' |
||
| 32 | -2x | +
- if (!identical(as.list(expr)[[1L]], as.symbol("{"))) {
+ #' @inheritParams init |
|
| 33 | -2x | +
- expr <- call("{", expr)
+ #' |
|
| 34 |
- }+ #' @return Invisible `NULL`. |
||
| 35 |
-
+ #' |
||
| 36 | -2x | +
- calls <- as.list(expr)[-1]+ #' @aliases bookmark bookmark_manager bookmark_manager_module |
|
| 37 |
-
+ #' |
||
| 38 |
- # Inject extra values into expressions.+ #' @name module_bookmark_manager |
||
| 39 | -2x | +
- calls <- lapply(calls, function(x) do.call(substitute, list(x, env = extras)))+ #' @rdname module_bookmark_manager |
|
| 40 |
-
+ #' |
||
| 41 | -2x | +
- eval_code(object = data, code = as.expression(calls))+ #' @keywords internal |
|
| 42 |
- }+ #' |
| 1 | +43 |
- #' Calls all `modules`+ NULL |
||
| 2 | +44 |
- #'+ |
||
| 3 | +45 |
- #' On the UI side each `teal_modules` is translated to a `tabsetPanel` and each `teal_module` is a+ #' @rdname module_bookmark_manager |
||
| 4 | +46 |
- #' `tabPanel`. Both, UI and server are called recursively so that each tab is a separate module and+ ui_bookmark_panel <- function(id, modules) {
|
||
| 5 | -+ | |||
| 47 | +! |
- #' reflect nested structure of `modules` argument.+ ns <- NS(id) |
||
| 6 | +48 |
- #'+ |
||
| 7 | -+ | |||
| 49 | +! |
- #' @name module_teal_module+ bookmark_option <- get_bookmarking_option() |
||
| 8 | -+ | |||
| 50 | +! |
- #'+ is_unbookmarkable <- need_bookmarking(modules) |
||
| 9 | -+ | |||
| 51 | +! |
- #' @inheritParams module_teal+ shinyOptions(bookmarkStore = bookmark_option) |
||
| 10 | +52 |
- #'+ |
||
| 11 | +53 |
- #' @param data_rv (`reactive` returning `teal_data`)+ # Render bookmark warnings count |
||
| 12 | -+ | |||
| 54 | +! |
- #'+ if (!all(is_unbookmarkable) && identical(bookmark_option, "server")) {
|
||
| 13 | -+ | |||
| 55 | +! |
- #' @param slices_global (`reactiveVal` returning `modules_teal_slices`)+ tags$button( |
||
| 14 | -+ | |||
| 56 | +! |
- #' see [`module_filter_manager`]+ id = ns("do_bookmark"),
|
||
| 15 | -+ | |||
| 57 | +! |
- #'+ class = "btn action-button wunder_bar_button bookmark_manager_button", |
||
| 16 | -+ | |||
| 58 | +! |
- #' @param depth (`integer(1)`)+ title = "Add bookmark", |
||
| 17 | -+ | |||
| 59 | +! |
- #' number which helps to determine depth of the modules nesting.+ tags$span( |
||
| 18 | -+ | |||
| 60 | +! |
- #'+ suppressMessages(icon("fas fa-bookmark")),
|
||
| 19 | -+ | |||
| 61 | +! |
- #' @param datasets (`reactive` returning `FilteredData` or `NULL`)+ if (any(is_unbookmarkable)) {
|
||
| 20 | -+ | |||
| 62 | +! |
- #' When `datasets` is passed from the parent module (`srv_teal`) then `dataset` is a singleton+ tags$span( |
||
| 21 | -+ | |||
| 63 | +! |
- #' which implies in filter-panel to be "global". When `NULL` then filter-panel is "module-specific".+ sum(is_unbookmarkable),+ |
+ ||
| 64 | +! | +
+ class = "badge-warning badge-count text-white bg-danger" |
||
| 22 | +65 |
- #'+ ) |
||
| 23 | +66 |
- #' @param data_load_status (`reactive` returning `character`)+ } |
||
| 24 | +67 |
- #' Determines action dependent on a data loading status:+ ) |
||
| 25 | +68 |
- #' - `"ok"` when `teal_data` is returned from the data loading.+ ) |
||
| 26 | +69 |
- #' - `"teal_data_module failed"` when [teal_data_module()] didn't return `teal_data`. Disables tabs buttons.+ } |
||
| 27 | +70 |
- #' - `"external failed"` when a `reactive` passed to `srv_teal(data)` didn't return `teal_data`. Hides the whole tab+ } |
||
| 28 | +71 |
- #' panel.+ |
||
| 29 | +72 |
- #'+ #' @rdname module_bookmark_manager |
||
| 30 | +73 |
- #' @return+ srv_bookmark_panel <- function(id, modules) {
+ |
+ ||
| 74 | +87x | +
+ checkmate::assert_character(id)+ |
+ ||
| 75 | +87x | +
+ checkmate::assert_class(modules, "teal_modules")+ |
+ ||
| 76 | +87x | +
+ moduleServer(id, function(input, output, session) {
+ |
+ ||
| 77 | +87x | +
+ logger::log_debug("bookmark_manager_srv initializing")
+ |
+ ||
| 78 | +87x | +
+ ns <- session$ns+ |
+ ||
| 79 | +87x | +
+ bookmark_option <- get_bookmarking_option()+ |
+ ||
| 80 | +87x | +
+ is_unbookmarkable <- need_bookmarking(modules) |
||
| 31 | +81 |
- #' output of currently active module.+ |
||
| 32 | +82 |
- #' - `srv_teal_module.teal_module` returns `reactiveVal` containing output of the called module.+ # Set up bookmarking callbacks ---- |
||
| 33 | +83 |
- #' - `srv_teal_module.teal_modules` returns output of module selected by `input$active_tab`.+ # Register bookmark exclusions: do_bookmark button to avoid re-bookmarking+ |
+ ||
| 84 | +87x | +
+ setBookmarkExclude(c("do_bookmark"))
|
||
| 34 | +85 |
- #'+ # This bookmark can only be used on the app session.+ |
+ ||
| 86 | +87x | +
+ app_session <- .subset2(session, "parent")+ |
+ ||
| 87 | +87x | +
+ app_session$onBookmarked(function(url) {
+ |
+ ||
| 88 | +! | +
+ 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 | +! | +
+ bookmark_option,+ |
+ ||
| 93 | +! | +
+ "Only server-side bookmarking is supported.",+ |
+ ||
| 94 | +! | +
+ "Please contact your app developer." |
||
| 35 | +95 |
- #' @keywords internal+ )+ |
+ ||
| 96 | +! | +
+ tags$div(+ |
+ ||
| 97 | +! | +
+ tags$p(msg, class = "text-warning") |
||
| 36 | +98 |
- NULL+ ) |
||
| 37 | +99 |
-
+ } else {
+ |
+ ||
| 100 | +! | +
+ tags$div(+ |
+ ||
| 101 | +! | +
+ tags$span(+ |
+ ||
| 102 | +! | +
+ tags$pre(url) |
||
| 38 | +103 |
- #' @rdname module_teal_module+ ), |
||
| 39 | -+ | |||
| 104 | +! |
- ui_teal_module <- function(id, modules, depth = 0L) {
+ if (any(is_unbookmarkable)) {
|
||
| 40 | +105 | ! |
- checkmate::assert_multi_class(modules, c("teal_modules", "teal_module", "shiny.tag"))
+ bkmb_summary <- rapply2( |
|
| 41 | +106 | ! |
- checkmate::assert_count(depth)+ modules_bookmarkable(modules), |
|
| 42 | +107 | ! |
- UseMethod("ui_teal_module", modules)
+ function(x) {
|
|
| 43 | -+ | |||
| 108 | +! |
- }+ if (isTRUE(x)) {
|
||
| 44 | -+ | |||
| 109 | +! |
-
+ "\u2705" # check mark |
||
| 45 | -+ | |||
| 110 | +! |
- #' @rdname module_teal_module+ } else if (isFALSE(x)) {
|
||
| 46 | -+ | |||
| 111 | +! |
- #' @export+ "\u274C" # cross mark |
||
| 47 | +112 |
- ui_teal_module.default <- function(id, modules, depth = 0L) {
+ } else {
|
||
| 48 | +113 | ! |
- stop("Modules class not supported: ", paste(class(modules), collapse = " "))
+ "\u2753" # question mark |
|
| 49 | +114 |
- }+ } |
||
| 50 | +115 |
-
+ } |
||
| 51 | +116 |
- #' @rdname module_teal_module+ ) |
||
| 52 | -+ | |||
| 117 | +! |
- #' @export+ tags$div( |
||
| 53 | -+ | |||
| 118 | +! |
- ui_teal_module.teal_modules <- function(id, modules, depth = 0L) {
+ tags$p( |
||
| 54 | +119 | ! |
- ns <- NS(id)+ icon("fas fa-exclamation-triangle"),
|
|
| 55 | +120 | ! |
- tags$div(+ "Some modules will not be restored when using this bookmark.", |
|
| 56 | +121 | ! |
- id = ns("wrapper"),
+ tags$br(), |
|
| 57 | +122 | ! |
- do.call(+ "Check the list below to see which modules are not bookmarkable.", |
|
| 58 | +123 | ! |
- tabsetPanel,+ class = "text-warning"+ |
+ |
| 124 | ++ |
+ ), |
||
| 59 | +125 | ! |
- c(+ tags$pre(yaml::as.yaml(bkmb_summary)) |
|
| 60 | +126 |
- # by giving an id, we can reactively respond to tab changes+ ) |
||
| 61 | -! | +|||
| 127 | +
- list(+ } |
|||
| 62 | -! | +|||
| 128 | +
- id = ns("active_tab"),
+ ) |
|||
| 63 | -! | +|||
| 129 | +
- type = if (modules$label == "root") "pills" else "tabs"+ } |
|||
| 64 | +130 |
- ),+ |
||
| 65 | +131 | ! |
- lapply(+ showModal( |
|
| 66 | +132 | ! |
- names(modules$children),+ modalDialog( |
|
| 67 | +133 | ! |
- function(module_id) {
+ id = ns("bookmark_modal"),
|
|
| 68 | +134 | ! |
- module_label <- modules$children[[module_id]]$label+ title = "Bookmarked teal app url", |
|
| 69 | +135 | ! |
- if (is.null(module_label)) {
+ modal_content, |
|
| 70 | +136 | ! |
- module_label <- icon("fas fa-database")
+ easyClose = TRUE |
|
| 71 | +137 |
- }+ ) |
||
| 72 | -! | +|||
| 138 | +
- tabPanel(+ ) |
|||
| 73 | -! | +|||
| 139 | +
- title = module_label,+ }) |
|||
| 74 | -! | +|||
| 140 | +
- value = module_id, # when clicked this tab value changes input$<tabset panel id>+ |
|||
| 75 | -! | +|||
| 141 | +
- ui_teal_module(+ # manually trigger bookmarking because of the problems reported on windows with bookmarkButton in teal |
|||
| 76 | -! | +|||
| 142 | +87x |
- id = ns(module_id),+ observeEvent(input$do_bookmark, {
|
||
| 77 | +143 | ! |
- modules = modules$children[[module_id]],+ logger::log_debug("bookmark_manager_srv@1 do_bookmark module clicked.")
|
|
| 78 | +144 | ! |
- depth = depth + 1L+ session$doBookmark() |
|
| 79 | +145 |
- )+ }) |
||
| 80 | +146 |
- )+ |
||
| 81 | -+ | |||
| 147 | +87x |
- }+ invisible(NULL) |
||
| 82 | +148 |
- )+ }) |
||
| 83 | +149 |
- )+ } |
||
| 84 | +150 |
- )+ |
||
| 85 | +151 |
- )+ |
||
| 86 | +152 |
- }+ #' @rdname module_bookmark_manager |
||
| 87 | +153 |
-
+ get_bookmarking_option <- function() {
|
||
| 88 | -+ | |||
| 154 | +87x |
- #' @rdname module_teal_module+ bookmark_option <- getShinyOption("bookmarkStore")
+ |
+ ||
| 155 | +87x | +
+ if (is.null(bookmark_option) && identical(getOption("shiny.bookmarkStore"), "server")) {
+ |
+ ||
| 156 | +! | +
+ bookmark_option <- getOption("shiny.bookmarkStore")
|
||
| 89 | +157 |
- #' @export+ }+ |
+ ||
| 158 | +87x | +
+ bookmark_option |
||
| 90 | +159 |
- ui_teal_module.teal_module <- function(id, modules, depth = 0L) {
+ } |
||
| 91 | -! | +|||
| 160 | +
- ns <- NS(id)+ |
|||
| 92 | -! | +|||
| 161 | +
- args <- c(list(id = ns("module")), modules$ui_args)
+ #' @rdname module_bookmark_manager |
|||
| 93 | +162 |
-
+ need_bookmarking <- function(modules) {
|
||
| 94 | -! | +|||
| 163 | +87x |
- ui_teal <- tagList(+ unlist(rapply2( |
||
| 95 | -! | +|||
| 164 | +87x |
- shinyjs::hidden(+ modules_bookmarkable(modules), |
||
| 96 | -! | +|||
| 165 | +87x |
- tags$div(+ Negate(isTRUE) |
||
| 97 | -! | +|||
| 166 | +
- id = ns("transform_failure_info"),
+ )) |
|||
| 98 | -! | +|||
| 167 | +
- class = "teal_validated",+ } |
|||
| 99 | -! | +|||
| 168 | +
- div(+ |
|||
| 100 | -! | +|||
| 169 | +
- class = "teal-output-warning",+ |
|||
| 101 | -! | +|||
| 170 | +
- "One of transformators failed. Please check its inputs."+ # utilities ---- |
|||
| 102 | +171 |
- )+ |
||
| 103 | +172 |
- )+ #' Restore value from bookmark. |
||
| 104 | +173 |
- ),+ #' |
||
| 105 | -! | +|||
| 174 | +
- tags$div(+ #' Get value from bookmark or return default. |
|||
| 106 | -! | +|||
| 175 | +
- id = ns("teal_module_ui"),
+ #' |
|||
| 107 | -! | +|||
| 176 | +
- tags$div(+ #' Bookmarks can store not only inputs but also arbitrary values. |
|||
| 108 | -! | +|||
| 177 | +
- class = "teal_validated",+ #' These values are stored by `onBookmark` callbacks and restored by `onBookmarked` callbacks, |
|||
| 109 | -! | +|||
| 178 | +
- ui_check_module_datanames(ns("validate_datanames"))
+ #' and they are placed in the `values` environment in the `session$restoreContext` field. |
|||
| 110 | +179 |
- ),+ #' Using `teal_data_module` makes it impossible to run the callbacks |
||
| 111 | -! | +|||
| 180 | +
- do.call(modules$ui, args)+ #' because the app becomes ready before modules execute and callbacks are registered. |
|||
| 112 | +181 |
- )+ #' In those cases the stored values can still be recovered from the `session` object directly. |
||
| 113 | +182 |
- )+ #' |
||
| 114 | +183 |
-
+ #' Note that variable names in the `values` environment are prefixed with module name space names, |
||
| 115 | -! | +|||
| 184 | +
- div(+ #' therefore, when using this function in modules, `value` must be run through the name space function. |
|||
| 116 | -! | +|||
| 185 | +
- id = id,+ #' |
|||
| 117 | -! | +|||
| 186 | +
- class = "teal_module",+ #' @param value (`character(1)`) name of value to restore |
|||
| 118 | -! | +|||
| 187 | +
- uiOutput(ns("data_reactive"), inline = TRUE),
+ #' @param default fallback value |
|||
| 119 | -! | +|||
| 188 | ++ |
+ #'+ |
+ ||
| 189 | +
- tagList(+ #' @return |
|||
| 120 | -! | +|||
| 190 | +
- if (depth >= 2L) tags$div(style = "mt-6"),+ #' In an application restored from a server-side bookmark, |
|||
| 121 | -! | +|||
| 191 | +
- if (!is.null(modules$datanames)) {
+ #' the variable specified by `value` from the `values` environment. |
|||
| 122 | -! | +|||
| 192 | +
- fluidRow(+ #' Otherwise `default`. |
|||
| 123 | -! | +|||
| 193 | +
- column(width = 9, ui_teal, class = "teal_primary_col"),+ #' |
|||
| 124 | -! | +|||
| 194 | +
- column(+ #' @keywords internal |
|||
| 125 | -! | +|||
| 195 | +
- width = 3,+ #' |
|||
| 126 | -! | +|||
| 196 | +
- ui_data_summary(ns("data_summary")),
+ restoreValue <- function(value, default) { # nolint: object_name.
|
|||
| 127 | -! | +|||
| 197 | +174x |
- ui_filter_data(ns("filter_panel")),
+ checkmate::assert_character("value")
|
||
| 128 | -! | +|||
| 198 | +174x |
- ui_transform_teal_data(ns("data_transform"), transformators = modules$transformators, class = "well"),
+ session_default <- shiny::getDefaultReactiveDomain() |
||
| 129 | -! | +|||
| 199 | +174x |
- class = "teal_secondary_col"+ session_parent <- .subset2(session_default, "parent") |
||
| 130 | -+ | |||
| 200 | +174x |
- )+ session <- if (is.null(session_parent)) session_default else session_parent |
||
| 131 | +201 |
- )+ |
||
| 132 | -+ | |||
| 202 | +174x |
- } else {
+ if (isTRUE(session$restoreContext$active) && exists(value, session$restoreContext$values, inherits = FALSE)) {
|
||
| 133 | +203 | ! |
- ui_teal+ session$restoreContext$values[[value]] |
|
| 134 | +204 |
- }+ } else {
|
||
| 135 | -+ | |||
| 205 | +174x |
- )+ default |
||
| 136 | +206 |
- )+ } |
||
| 137 | +207 |
} |
||
| 138 | +208 | |||
| 139 | +209 |
- #' @rdname module_teal_module+ #' Compare bookmarks. |
||
| 140 | +210 |
- srv_teal_module <- function(id,+ #' |
||
| 141 | +211 |
- data_rv,+ #' Test if two bookmarks store identical state. |
||
| 142 | +212 |
- modules,+ #' |
||
| 143 | +213 |
- datasets = NULL,+ #' `input` environments are compared one variable at a time and if not identical, |
||
| 144 | +214 |
- slices_global,+ #' values in both bookmarks are reported. States of `datatable`s are stripped |
||
| 145 | +215 |
- reporter = teal.reporter::Reporter$new(),+ #' of the `time` element before comparing because the time stamp is always different. |
||
| 146 | +216 |
- data_load_status = reactive("ok"),
+ #' The contents themselves are not printed as they are large and the contents are not informative. |
||
| 147 | +217 |
- is_active = reactive(TRUE)) {
+ #' Elements present in one bookmark and absent in the other are also reported. |
||
| 148 | -199x | +|||
| 218 | +
- checkmate::assert_string(id)+ #' Differences are printed as messages. |
|||
| 149 | -199x | +|||
| 219 | +
- assert_reactive(data_rv)+ #' |
|||
| 150 | -199x | +|||
| 220 | +
- checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"))
+ #' `values` environments are compared with `all.equal`. |
|||
| 151 | -199x | +|||
| 221 | +
- assert_reactive(datasets, null.ok = TRUE)+ #' |
|||
| 152 | -199x | +|||
| 222 | +
- checkmate::assert_class(slices_global, ".slicesGlobal")+ #' @section How to use: |
|||
| 153 | -199x | +|||
| 223 | +
- checkmate::assert_class(reporter, "Reporter")+ #' Open an application, change relevant inputs (typically, all of them), and create a bookmark. |
|||
| 154 | -199x | +|||
| 224 | +
- assert_reactive(data_load_status)+ #' Then open that bookmark and immediately create a bookmark of that. |
|||
| 155 | -199x | +|||
| 225 | +
- UseMethod("srv_teal_module", modules)
+ #' If restoring bookmarks occurred properly, the two bookmarks should store the same state. |
|||
| 156 | +226 |
- }+ #' |
||
| 157 | +227 |
-
+ #' |
||
| 158 | +228 |
- #' @rdname module_teal_module+ #' @param book1,book2 bookmark directories stored in `shiny_bookmarks/`; |
||
| 159 | +229 |
- #' @export+ #' default to the two most recently modified directories |
||
| 160 | +230 |
- srv_teal_module.default <- function(id,+ #' |
||
| 161 | +231 |
- data_rv,+ #' @return |
||
| 162 | +232 |
- modules,+ #' Invisible `NULL` if bookmarks are identical or if there are no bookmarks to test. |
||
| 163 | +233 |
- datasets = NULL,+ #' `FALSE` if inconsistencies are detected. |
||
| 164 | +234 |
- slices_global,+ #' |
||
| 165 | +235 |
- reporter = teal.reporter::Reporter$new(),+ #' @keywords internal |
||
| 166 | +236 |
- data_load_status = reactive("ok"),
+ #' |
||
| 167 | +237 |
- is_active = reactive(TRUE)) {
+ bookmarks_identical <- function(book1, book2) {
|
||
| 168 | +238 | ! |
- stop("Modules class not supported: ", paste(class(modules), collapse = " "))
+ if (!dir.exists("shiny_bookmarks")) {
+ |
+ |
| 239 | +! | +
+ message("no bookmark directory")
+ |
+ ||
| 240 | +! | +
+ return(invisible(NULL)) |
||
| 169 | +241 |
- }+ } |
||
| 170 | +242 | |||
| 171 | -+ | |||
| 243 | +! |
- #' @rdname module_teal_module+ ans <- TRUE |
||
| 172 | +244 |
- #' @export+ |
||
| 173 | -+ | |||
| 245 | +! |
- srv_teal_module.teal_modules <- function(id,+ if (missing(book1) && missing(book2)) {
|
||
| 174 | -+ | |||
| 246 | +! |
- data_rv,+ dirs <- list.dirs("shiny_bookmarks", recursive = FALSE)
|
||
| 175 | -+ | |||
| 247 | +! |
- modules,+ bookmarks_sorted <- basename(rev(dirs[order(file.mtime(dirs))])) |
||
| 176 | -+ | |||
| 248 | +! |
- datasets = NULL,+ if (length(bookmarks_sorted) < 2L) {
+ |
+ ||
| 249 | +! | +
+ message("no bookmarks to compare")
+ |
+ ||
| 250 | +! | +
+ return(invisible(NULL)) |
||
| 177 | +251 |
- slices_global,+ }+ |
+ ||
| 252 | +! | +
+ book1 <- bookmarks_sorted[2L]+ |
+ ||
| 253 | +! | +
+ book2 <- bookmarks_sorted[1L] |
||
| 178 | +254 |
- reporter = teal.reporter::Reporter$new(),+ } else {
+ |
+ ||
| 255 | +! | +
+ if (!dir.exists(file.path("shiny_bookmarks", book1))) stop(book1, " not found")
+ |
+ ||
| 256 | +! | +
+ if (!dir.exists(file.path("shiny_bookmarks", book2))) stop(book2, " not found")
|
||
| 179 | +257 |
- data_load_status = reactive("ok"),
+ } |
||
| 180 | +258 |
- is_active = reactive(TRUE)) {
+
|
||
| 181 | -87x | +|||
| 259 | +! |
- moduleServer(id = id, module = function(input, output, session) {
+ book1_input <- readRDS(file.path("shiny_bookmarks", book1, "input.rds"))
|
||
| 182 | -87x | +|||
| 260 | +! |
- logger::log_debug("srv_teal_module.teal_modules initializing the module { deparse1(modules$label) }.")
+ book2_input <- readRDS(file.path("shiny_bookmarks", book2, "input.rds"))
|
||
| 183 | +261 | |||
| 184 | -87x | +|||
| 262 | +! |
- observeEvent(data_load_status(), {
+ elements_common <- intersect(names(book1_input), names(book2_input)) |
||
| 185 | -80x | +|||
| 263 | +! |
- tabs_selector <- sprintf("#%s li a", session$ns("active_tab"))
+ dt_states <- grepl("_state$", elements_common)
|
||
| 186 | -80x | +|||
| 264 | +! |
- if (identical(data_load_status(), "ok")) {
+ if (any(dt_states)) {
|
||
| 187 | -75x | +|||
| 265 | +! |
- logger::log_debug("srv_teal_module@1 enabling modules tabs.")
+ for (el in elements_common[dt_states]) {
|
||
| 188 | -75x | +|||
| 266 | +! |
- shinyjs::show("wrapper")
+ book1_input[[el]][["time"]] <- NULL |
||
| 189 | -75x | +|||
| 267 | +! |
- shinyjs::enable(selector = tabs_selector)+ book2_input[[el]][["time"]] <- NULL |
||
| 190 | -5x | +|||
| 268 | +
- } else if (identical(data_load_status(), "teal_data_module failed")) {
+ } |
|||
| 191 | -5x | +|||
| 269 | +
- logger::log_debug("srv_teal_module@1 disabling modules tabs.")
+ } |
|||
| 192 | -5x | +|||
| 270 | +
- shinyjs::disable(selector = tabs_selector)+ |
|||
| 193 | +271 | +! | +
+ identicals <- mapply(identical, book1_input[elements_common], book2_input[elements_common])+ |
+ |
| 272 | +! | +
+ non_identicals <- names(identicals[!identicals])+ |
+ ||
| 273 | +! | +
+ compares <- sprintf("$ %s:\t%s --- %s", non_identicals, book1_input[non_identicals], book2_input[non_identicals])
+ |
+ ||
| 274 | ! |
- } else if (identical(data_load_status(), "external failed")) {
+ if (length(compares) != 0L) {
|
||
| 194 | +275 | ! |
- logger::log_debug("srv_teal_module@1 hiding modules tabs.")
+ message("common elements not identical: \n", paste(compares, collapse = "\n"))
|
|
| 195 | +276 | ! |
- shinyjs::hide("wrapper")
+ ans <- FALSE |
|
| 196 | +277 |
- }+ } |
||
| 197 | +278 |
- })+ |
||
| 198 | -+ | |||
| 279 | +! |
-
+ elements_boook1 <- setdiff(names(book1_input), names(book2_input)) |
||
| 199 | -87x | +|||
| 280 | +! |
- modules_output <- sapply(+ if (length(elements_boook1) != 0L) {
|
||
| 200 | -87x | +|||
| 281 | +! |
- names(modules$children),+ dt_states <- grepl("_state$", elements_boook1)
|
||
| 201 | -87x | +|||
| 282 | +! |
- function(module_id) {
+ if (any(dt_states)) {
|
||
| 202 | -112x | +|||
| 283 | +! |
- srv_teal_module(+ for (el in elements_boook1[dt_states]) {
|
||
| 203 | -112x | +|||
| 284 | +! |
- id = module_id,+ if (is.list(book1_input[[el]])) book1_input[[el]] <- "--- data table state ---" |
||
| 204 | -112x | +|||
| 285 | +
- data_rv = data_rv,+ } |
|||
| 205 | -112x | +|||
| 286 | +
- modules = modules$children[[module_id]],+ } |
|||
| 206 | -112x | +|||
| 287 | +! |
- datasets = datasets,+ excess1 <- sprintf("$ %s:\t%s", elements_boook1, book1_input[elements_boook1])
|
||
| 207 | -112x | +|||
| 288 | +! |
- slices_global = slices_global,+ message("elements only in book1: \n", paste(excess1, collapse = "\n"))
|
||
| 208 | -112x | +|||
| 289 | +! |
- reporter = reporter,+ ans <- FALSE |
||
| 209 | -112x | +|||
| 290 | +
- is_active = reactive(+ } |
|||
| 210 | -112x | +|||
| 291 | +
- is_active() &&+ |
|||
| 211 | -112x | +|||
| 292 | +! |
- input$active_tab == module_id &&+ elements_boook2 <- setdiff(names(book2_input), names(book1_input)) |
||
| 212 | -112x | +|||
| 293 | +! |
- identical(data_load_status(), "ok")+ if (length(elements_boook2) != 0L) {
|
||
| 213 | -+ | |||
| 294 | +! |
- )+ dt_states <- grepl("_state$", elements_boook1)
|
||
| 214 | -+ | |||
| 295 | +! |
- )+ if (any(dt_states)) {
|
||
| 215 | -+ | |||
| 296 | +! |
- },+ for (el in elements_boook1[dt_states]) {
|
||
| 216 | -87x | +|||
| 297 | +! |
- simplify = FALSE+ if (is.list(book2_input[[el]])) book2_input[[el]] <- "--- data table state ---" |
||
| 217 | +298 |
- )+ } |
||
| 218 | +299 |
-
+ } |
||
| 219 | -87x | +|||
| 300 | +! |
- modules_output+ excess2 <- sprintf("$ %s:\t%s", elements_boook2, book2_input[elements_boook2])
|
||
| 220 | -+ | |||
| 301 | +! |
- })+ message("elements only in book2: \n", paste(excess2, collapse = "\n"))
|
||
| 221 | -+ | |||
| 302 | +! |
- }+ ans <- FALSE |
||
| 222 | +303 |
-
+ } |
||
| 223 | +304 |
- #' @rdname module_teal_module+ |
||
| 224 | -+ | |||
| 305 | +! |
- #' @export+ book1_values <- readRDS(file.path("shiny_bookmarks", book1, "values.rds"))
|
||
| 225 | -+ | |||
| 306 | +! |
- srv_teal_module.teal_module <- function(id,+ book2_values <- readRDS(file.path("shiny_bookmarks", book2, "values.rds"))
|
||
| 226 | +307 |
- data_rv,+ |
||
| 227 | -+ | |||
| 308 | +! |
- modules,+ if (!isTRUE(all.equal(book1_values, book2_values))) {
|
||
| 228 | -+ | |||
| 309 | +! |
- datasets = NULL,+ message("different values detected")
|
||
| 229 | -+ | |||
| 310 | +! |
- slices_global,+ message("choices for numeric filters MAY be different, see RangeFilterState$set_choices")
|
||
| 230 | -+ | |||
| 311 | +! |
- reporter = teal.reporter::Reporter$new(),+ ans <- FALSE |
||
| 231 | +312 |
- data_load_status = reactive("ok"),
+ } |
||
| 232 | +313 |
- is_active = reactive(TRUE)) {
+
|
||
| 233 | -112x | +|||
| 314 | +! |
- logger::log_debug("srv_teal_module.teal_module initializing the module: { deparse1(modules$label) }.")
+ if (ans) message("perfect!")
|
||
| 234 | -112x | +|||
| 315 | +! |
- moduleServer(id = id, module = function(input, output, session) {
+ invisible(NULL) |
||
| 235 | -112x | +|||
| 316 | +
- module_out <- reactiveVal()+ } |
|||
| 236 | +317 | |||
| 237 | -112x | +|||
| 318 | +
- active_datanames <- reactive({
+
|
|||
| 238 | -89x | +|||
| 319 | +
- .resolve_module_datanames(data = data_rv(), modules = modules)+ # Replacement for [base::rapply] which doesn't handle NULL values - skips the evaluation |
|||
| 239 | +320 |
- })+ # of the function and returns NULL for given element. |
||
| 240 | -112x | +|||
| 321 | +
- if (is.null(datasets)) {
+ rapply2 <- function(x, f) {
|
|||
| 241 | -20x | +322 | +199x |
- datasets <- eventReactive(data_rv(), {
+ if (inherits(x, "list")) {
|
| 242 | -16x | +323 | +87x |
- req(inherits(data_rv(), "teal_data"))+ lapply(x, rapply2, f = f) |
| 243 | -16x | +|||
| 324 | +
- logger::log_debug("srv_teal_module@1 initializing module-specific FilteredData")
+ } else {
|
|||
| 244 | -16x | +325 | +112x |
- teal_data_to_filtered_data(data_rv(), datanames = active_datanames())+ f(x) |
| 245 | +326 |
- })+ } |
||
| 246 | +327 |
- }+ } |
| 247 | +1 |
-
+ #' Validate that dataset has a minimum number of observations |
||
| 248 | +2 |
- # manage module filters on the module level+ #' |
||
| 249 | +3 |
- # important:+ #' `r lifecycle::badge("stable")`
|
||
| 250 | +4 |
- # filter_manager_module_srv needs to be called before filter_panel_srv+ #' |
||
| 251 | +5 |
- # Because available_teal_slices is used in FilteredData$srv_available_slices (via srv_filter_panel)+ #' This function is a wrapper for `shiny::validate`. |
||
| 252 | +6 |
- # and if it is not set, then it won't be available in the srv_filter_panel+ #' |
||
| 253 | -112x | +|||
| 7 | +
- srv_module_filter_manager(modules$label, module_fd = datasets, slices_global = slices_global)+ #' @param x (`data.frame`) |
|||
| 254 | +8 |
-
+ #' @param min_nrow (`numeric(1)`) Minimum allowed number of rows in `x`. |
||
| 255 | -112x | +|||
| 9 | +
- call_once_when(is_active(), {
+ #' @param complete (`logical(1)`) Flag specifying whether to check only complete cases. Defaults to `FALSE`. |
|||
| 256 | -86x | +|||
| 10 | +
- filtered_teal_data <- srv_filter_data(+ #' @param allow_inf (`logical(1)`) Flag specifying whether to allow infinite values. Defaults to `TRUE`. |
|||
| 257 | -86x | +|||
| 11 | +
- "filter_panel",+ #' @param msg (`character(1)`) Additional message to display alongside the default message. |
|||
| 258 | -86x | +|||
| 12 | +
- datasets = datasets,+ #' |
|||
| 259 | -86x | +|||
| 13 | +
- active_datanames = active_datanames,+ #' @export |
|||
| 260 | -86x | +|||
| 14 | +
- data_rv = data_rv,+ #' |
|||
| 261 | -86x | +|||
| 15 | +
- is_active = is_active+ #' @examples |
|||
| 262 | +16 |
- )+ #' library(teal) |
||
| 263 | -86x | +|||
| 17 | +
- is_transform_failed <- reactiveValues()+ #' ui <- fluidPage( |
|||
| 264 | -86x | +|||
| 18 | +
- transformed_teal_data <- srv_transform_teal_data(+ #' sliderInput("len", "Max Length of Sepal",
|
|||
| 265 | -86x | +|||
| 19 | +
- "data_transform",+ #' min = 4.3, max = 7.9, value = 5 |
|||
| 266 | -86x | +|||
| 20 | +
- data = filtered_teal_data,+ #' ), |
|||
| 267 | -86x | +|||
| 21 | +
- transformators = modules$transformators,+ #' plotOutput("plot")
|
|||
| 268 | -86x | +|||
| 22 | +
- modules = modules,+ #' ) |
|||
| 269 | -86x | +|||
| 23 | +
- is_transform_failed = is_transform_failed+ #' |
|||
| 270 | +24 |
- )+ #' server <- function(input, output) {
|
||
| 271 | -86x | +|||
| 25 | +
- any_transform_failed <- reactive({
+ #' output$plot <- renderPlot({
|
|||
| 272 | -86x | +|||
| 26 | +
- any(unlist(reactiveValuesToList(is_transform_failed)))+ #' iris_df <- iris[iris$Sepal.Length <= input$len, ] |
|||
| 273 | +27 |
- })+ #' validate_has_data( |
||
| 274 | +28 |
-
+ #' iris_df, |
||
| 275 | -86x | +|||
| 29 | +
- observeEvent(any_transform_failed(), {
+ #' min_nrow = 10, |
|||
| 276 | -86x | +|||
| 30 | +
- if (isTRUE(any_transform_failed())) {
+ #' complete = FALSE, |
|||
| 277 | -6x | +|||
| 31 | +
- shinyjs::hide("teal_module_ui")
+ #' msg = "Please adjust Max Length of Sepal" |
|||
| 278 | -6x | +|||
| 32 | +
- shinyjs::show("transform_failure_info")
+ #' ) |
|||
| 279 | +33 |
- } else {
+ #' |
||
| 280 | -80x | +|||
| 34 | +
- shinyjs::show("teal_module_ui")
+ #' hist(iris_df$Sepal.Length, breaks = 5) |
|||
| 281 | -80x | +|||
| 35 | +
- shinyjs::hide("transform_failure_info")
+ #' }) |
|||
| 282 | +36 |
- }+ #' } |
||
| 283 | +37 |
- })+ #' if (interactive()) {
|
||
| 284 | +38 |
-
+ #' shinyApp(ui, server) |
||
| 285 | -86x | +|||
| 39 | +
- module_teal_data <- reactive({
+ #' } |
|||
| 286 | -94x | +|||
| 40 | +
- req(inherits(transformed_teal_data(), "teal_data"))+ #' |
|||
| 287 | -88x | +|||
| 41 | +
- all_teal_data <- transformed_teal_data()+ validate_has_data <- function(x, |
|||
| 288 | -88x | +|||
| 42 | +
- module_datanames <- .resolve_module_datanames(data = all_teal_data, modules = modules)+ min_nrow = NULL, |
|||
| 289 | -88x | +|||
| 43 | +
- all_teal_data[c(module_datanames, ".raw_data")]+ complete = FALSE, |
|||
| 290 | +44 |
- })+ allow_inf = TRUE, |
||
| 291 | +45 |
-
+ msg = NULL) {
|
||
| 292 | -86x | +46 | +17x |
- srv_check_module_datanames(+ checkmate::assert_string(msg, null.ok = TRUE) |
| 293 | -86x | +47 | +15x |
- "validate_datanames",+ checkmate::assert_data_frame(x) |
| 294 | -86x | +48 | +15x |
- data = module_teal_data,+ if (!is.null(min_nrow)) {
|
| 295 | -86x | +49 | +15x |
- modules = modules+ if (complete) {
|
| 296 | -+ | |||
| 50 | +5x |
- )+ complete_index <- stats::complete.cases(x) |
||
| 297 | -+ | |||
| 51 | +5x |
-
+ validate(need( |
||
| 298 | -86x | +52 | +5x |
- summary_table <- srv_data_summary("data_summary", module_teal_data)
+ sum(complete_index) > 0 && nrow(x[complete_index, , drop = FALSE]) >= min_nrow, |
| 299 | -+ | |||
| 53 | +5x |
-
+ paste(c(paste("Number of complete cases is less than:", min_nrow), msg), collapse = "\n")
|
||
| 300 | +54 |
- # Call modules.+ )) |
||
| 301 | -86x | +|||
| 55 | +
- if (!inherits(modules, "teal_module_previewer")) {
+ } else {
|
|||
| 302 | -86x | +56 | +10x |
- obs_module <- call_once_when(+ validate(need( |
| 303 | -86x | +57 | +10x |
- !is.null(module_teal_data()),+ nrow(x) >= min_nrow, |
| 304 | -86x | +58 | +10x |
- ignoreNULL = TRUE,+ paste( |
| 305 | -86x | +59 | +10x |
- handlerExpr = {
+ c(paste("Minimum number of records not met: >=", min_nrow, "records required."), msg),
|
| 306 | -80x | +60 | +10x |
- module_out(.call_teal_module(modules, datasets, module_teal_data, reporter))+ collapse = "\n" |
| 307 | +61 |
- }+ ) |
||
| 308 | +62 |
- )+ )) |
||
| 309 | +63 |
- } else {
+ } |
||
| 310 | +64 |
- # Report previewer must be initiated on app start for report cards to be included in bookmarks.+ |
||
| 311 | -+ | |||
| 65 | +10x |
- # When previewer is delayed, cards are bookmarked only if previewer has been initiated (visited).+ if (!allow_inf) {
|
||
| 312 | -! | +|||
| 66 | +6x |
- module_out(.call_teal_module(modules, datasets, module_teal_data, reporter))+ validate(need( |
||
| 313 | -+ | |||
| 67 | +6x |
- }+ all(vapply(x, function(col) !is.numeric(col) || !any(is.infinite(col)), logical(1))), |
||
| 314 | -+ | |||
| 68 | +6x |
- })+ "Dataframe contains Inf values which is not allowed." |
||
| 315 | +69 |
-
+ )) |
||
| 316 | -112x | +|||
| 70 | +
- module_out+ } |
|||
| 317 | +71 |
- })+ } |
||
| 318 | +72 |
} |
||
| 319 | +73 | |||
| 320 | +74 |
- # This function calls a module server function.+ #' Validate that dataset has unique rows for key variables |
||
| 321 | +75 |
- .call_teal_module <- function(modules, datasets, filtered_teal_data, reporter) {
+ #' |
||
| 322 | +76 |
- # collect arguments to run teal_module- |
- ||
| 323 | -80x | -
- args <- c(list(id = "module"), modules$server_args)- |
- ||
| 324 | -80x | -
- if (is_arg_used(modules$server, "reporter")) {
- |
- ||
| 325 | -1x | -
- args <- c(args, list(reporter = reporter))+ #' `r lifecycle::badge("stable")`
|
||
| 326 | +77 |
- }+ #' |
||
| 327 | +78 | - - | -||
| 328 | -80x | -
- if (is_arg_used(modules$server, "datasets")) {
- |
- ||
| 329 | -1x | -
- args <- c(args, datasets = datasets())- |
- ||
| 330 | -1x | -
- warning("datasets argument is not reactive and therefore it won't be updated when data is refreshed.")
+ #' This function is a wrapper for `shiny::validate`. |
||
| 331 | +79 |
- }+ #' |
||
| 332 | +80 | - - | -||
| 333 | -80x | -
- if (is_arg_used(modules$server, "data")) {
+ #' @param x (`data.frame`) |
||
| 334 | -76x | +|||
| 81 | +
- args <- c(args, data = list(filtered_teal_data))+ #' @param key (`character`) Vector of ID variables from `x` that identify unique records. |
|||
| 335 | +82 |
- }+ #' |
||
| 336 | +83 |
-
+ #' @export |
||
| 337 | -80x | +|||
| 84 | +
- if (is_arg_used(modules$server, "filter_panel_api")) {
+ #' |
|||
| 338 | -1x | +|||
| 85 | +
- args <- c(args, filter_panel_api = teal.slice::FilterPanelAPI$new(datasets()))+ #' @examples |
|||
| 339 | +86 |
- }+ #' iris$id <- rep(1:50, times = 3) |
||
| 340 | +87 |
-
+ #' ui <- fluidPage( |
||
| 341 | -80x | +|||
| 88 | +
- if (is_arg_used(modules$server, "id")) {
+ #' selectInput( |
|||
| 342 | -80x | +|||
| 89 | +
- do.call(modules$server, args)+ #' inputId = "species", |
|||
| 343 | +90 |
- } else {
+ #' label = "Select species", |
||
| 344 | -! | +|||
| 91 | +
- do.call(callModule, c(args, list(module = modules$server)))+ #' choices = c("setosa", "versicolor", "virginica"),
|
|||
| 345 | +92 |
- }+ #' selected = "setosa", |
||
| 346 | +93 |
- }+ #' multiple = TRUE |
||
| 347 | +94 |
-
+ #' ), |
||
| 348 | +95 |
- .resolve_module_datanames <- function(data, modules) {
+ #' plotOutput("plot")
|
||
| 349 | -177x | +|||
| 96 | +
- stopifnot("data_rv must be teal_data object." = inherits(data, "teal_data"))
+ #' ) |
|||
| 350 | -177x | +|||
| 97 | +
- if (is.null(modules$datanames) || identical(modules$datanames, "all")) {
+ #' server <- function(input, output) {
|
|||
| 351 | -145x | +|||
| 98 | +
- names(data)+ #' output$plot <- renderPlot({
|
|||
| 352 | +99 |
- } else {
+ #' iris_f <- iris[iris$Species %in% input$species, ] |
||
| 353 | -32x | +|||
| 100 | +
- intersect(+ #' validate_one_row_per_id(iris_f, key = c("id"))
|
|||
| 354 | -32x | +|||
| 101 | +
- names(data), # Keep topological order from teal.data::names()+ #' |
|||
| 355 | -32x | +|||
| 102 | +
- .include_parent_datanames(modules$datanames, teal.data::join_keys(data))+ #' hist(iris_f$Sepal.Length, breaks = 5) |
|||
| 356 | +103 |
- )+ #' }) |
||
| 357 | +104 |
- }+ #' } |
||
| 358 | +105 |
- }+ #' if (interactive()) {
|
||
| 359 | +106 |
-
+ #' shinyApp(ui, server) |
||
| 360 | +107 |
- #' Calls expression when condition is met+ #' } |
||
| 361 | +108 |
#' |
||
| 362 | +109 |
- #' Function postpones `handlerExpr` to the moment when `eventExpr` (condition) returns `TRUE`,+ validate_one_row_per_id <- function(x, key = c("USUBJID", "STUDYID")) {
|
||
| 363 | -+ | |||
| 110 | +! |
- #' otherwise nothing happens.+ validate(need(!any(duplicated(x[key])), paste("Found more than one row per id.")))
|
||
| 364 | +111 |
- #' @param eventExpr A (quoted or unquoted) logical expression that represents the event;+ } |
||
| 365 | +112 |
- #' this can be a simple reactive value like input$click, a call to a reactive expression+ |
||
| 366 | +113 |
- #' like dataset(), or even a complex expression inside curly braces.+ #' Validates that vector includes all expected values |
||
| 367 | +114 |
- #' @param ... additional arguments passed to `observeEvent` with the exception of `eventExpr` that is not allowed.+ #' |
||
| 368 | +115 |
- #' @inheritParams shiny::observeEvent+ #' `r lifecycle::badge("stable")`
|
||
| 369 | +116 |
#' |
||
| 370 | +117 |
- #' @return An observer.+ #' This function is a wrapper for `shiny::validate`. |
||
| 371 | +118 |
#' |
||
| 372 | +119 |
- #' @keywords internal+ #' @param x Vector of values to test. |
||
| 373 | +120 |
- call_once_when <- function(eventExpr, # nolint: object_name.+ #' @param choices Vector to test against. |
||
| 374 | +121 |
- handlerExpr, # nolint: object_name.+ #' @param msg (`character(1)`) Error message to display if some elements of `x` are not elements of `choices`. |
||
| 375 | +122 |
- event.env = parent.frame(), # nolint: object_name.+ #' |
||
| 376 | +123 |
- handler.env = parent.frame(), # nolint: object_name.+ #' @export |
||
| 377 | +124 |
- ...) {
- |
- ||
| 378 | -198x | -
- event_quo <- rlang::new_quosure(substitute(eventExpr), env = event.env)+ #' |
||
| 379 | -198x | +|||
| 125 | +
- handler_quo <- rlang::new_quosure(substitute(handlerExpr), env = handler.env)+ #' @examples |
|||
| 380 | +126 |
-
+ #' ui <- fluidPage( |
||
| 381 | +127 |
- # When `condExpr` is TRUE, then `handlerExpr` is evaluated once.+ #' selectInput( |
||
| 382 | -198x | +|||
| 128 | +
- activator <- reactive({
+ #' "species", |
|||
| 383 | -198x | +|||
| 129 | +
- if (isTRUE(rlang::eval_tidy(event_quo))) {
+ #' "Select species", |
|||
| 384 | -166x | +|||
| 130 | +
- TRUE+ #' choices = c("setosa", "versicolor", "virginica", "unknown species"),
|
|||
| 385 | +131 |
- }+ #' selected = "setosa", |
||
| 386 | +132 |
- })+ #' multiple = FALSE |
||
| 387 | +133 |
-
+ #' ), |
||
| 388 | -198x | +|||
| 134 | +
- observeEvent(+ #' verbatimTextOutput("summary")
|
|||
| 389 | -198x | +|||
| 135 | +
- eventExpr = activator(),+ #' ) |
|||
| 390 | -198x | +|||
| 136 | +
- once = TRUE,+ #' |
|||
| 391 | -198x | +|||
| 137 | +
- handlerExpr = rlang::eval_tidy(handler_quo),+ #' server <- function(input, output) {
|
|||
| 392 | +138 |
- ...+ #' output$summary <- renderPrint({
|
||
| 393 | +139 |
- )+ #' validate_in(input$species, iris$Species, "Species does not exist.") |
||
| 394 | +140 |
- }+ #' nrow(iris[iris$Species == input$species, ]) |
| 1 | +141 |
- #' Validate that dataset has a minimum number of observations+ #' }) |
|
| 2 | +142 |
- #'+ #' } |
|
| 3 | +143 |
- #' `r lifecycle::badge("stable")`
+ #' if (interactive()) {
|
|
| 4 | +144 |
- #'+ #' shinyApp(ui, server) |
|
| 5 | +145 |
- #' This function is a wrapper for `shiny::validate`.+ #' } |
|
| 6 | +146 |
#' |
|
| 7 | +147 |
- #' @param x (`data.frame`)+ validate_in <- function(x, choices, msg) {
|
|
| 8 | -+ | ||
| 148 | +! |
- #' @param min_nrow (`numeric(1)`) Minimum allowed number of rows in `x`.+ validate(need(length(x) > 0 && length(choices) > 0 && all(x %in% choices), msg)) |
|
| 9 | +149 |
- #' @param complete (`logical(1)`) Flag specifying whether to check only complete cases. Defaults to `FALSE`.+ } |
|
| 10 | +150 |
- #' @param allow_inf (`logical(1)`) Flag specifying whether to allow infinite values. Defaults to `TRUE`.+ |
|
| 11 | +151 |
- #' @param msg (`character(1)`) Additional message to display alongside the default message.+ #' Validates that vector has length greater than 0 |
|
| 12 | +152 |
#' |
|
| 13 | +153 |
- #' @export+ #' `r lifecycle::badge("stable")`
|
|
| 14 | +154 |
#' |
|
| 15 | +155 |
- #' @examples+ #' This function is a wrapper for `shiny::validate`. |
|
| 16 | +156 |
- #' library(teal)+ #' |
|
| 17 | +157 |
- #' ui <- fluidPage(+ #' @param x vector |
|
| 18 | +158 |
- #' sliderInput("len", "Max Length of Sepal",
+ #' @param msg message to display |
|
| 19 | +159 |
- #' min = 4.3, max = 7.9, value = 5+ #' |
|
| 20 | +160 |
- #' ),+ #' @export |
|
| 21 | +161 |
- #' plotOutput("plot")
+ #' |
|
| 22 | +162 |
- #' )+ #' @examples |
|
| 23 | +163 |
- #'+ #' data <- data.frame( |
|
| 24 | +164 |
- #' server <- function(input, output) {
+ #' id = c(1:10, 11:20, 1:10), |
|
| 25 | +165 |
- #' output$plot <- renderPlot({
+ #' strata = rep(c("A", "B"), each = 15)
|
|
| 26 | +166 |
- #' iris_df <- iris[iris$Sepal.Length <= input$len, ]+ #' ) |
|
| 27 | +167 |
- #' validate_has_data(+ #' ui <- fluidPage( |
|
| 28 | +168 |
- #' iris_df,+ #' selectInput("ref1", "Select strata1 to compare",
|
|
| 29 | +169 |
- #' min_nrow = 10,+ #' choices = c("A", "B", "C"), selected = "A"
|
|
| 30 | +170 |
- #' complete = FALSE,+ #' ), |
|
| 31 | +171 |
- #' msg = "Please adjust Max Length of Sepal"+ #' selectInput("ref2", "Select strata2 to compare",
|
|
| 32 | +172 |
- #' )+ #' choices = c("A", "B", "C"), selected = "B"
|
|
| 33 | +173 |
- #'+ #' ), |
|
| 34 | +174 |
- #' hist(iris_df$Sepal.Length, breaks = 5)+ #' verbatimTextOutput("arm_summary")
|
|
| 35 | +175 |
- #' })+ #' ) |
|
| 36 | +176 |
- #' }+ #' |
|
| 37 | +177 |
- #' if (interactive()) {
+ #' server <- function(input, output) {
|
|
| 38 | +178 |
- #' shinyApp(ui, server)+ #' output$arm_summary <- renderText({
|
|
| 39 | +179 |
- #' }+ #' sample_1 <- data$id[data$strata == input$ref1] |
|
| 40 | +180 |
- #'+ #' sample_2 <- data$id[data$strata == input$ref2] |
|
| 41 | +181 |
- validate_has_data <- function(x,+ #' |
|
| 42 | +182 |
- min_nrow = NULL,+ #' validate_has_elements(sample_1, "No subjects in strata1.") |
|
| 43 | +183 |
- complete = FALSE,+ #' validate_has_elements(sample_2, "No subjects in strata2.") |
|
| 44 | +184 |
- allow_inf = TRUE,+ #' |
|
| 45 | +185 |
- msg = NULL) {
- |
- |
| 46 | -17x | -
- checkmate::assert_string(msg, null.ok = TRUE)- |
- |
| 47 | -15x | -
- checkmate::assert_data_frame(x)+ #' paste0( |
|
| 48 | -15x | +||
| 186 | +
- if (!is.null(min_nrow)) {
+ #' "Number of samples in: strata1=", length(sample_1), |
||
| 49 | -15x | +||
| 187 | +
- if (complete) {
+ #' " comparions strata2=", length(sample_2) |
||
| 50 | -5x | +||
| 188 | +
- complete_index <- stats::complete.cases(x)+ #' ) |
||
| 51 | -5x | +||
| 189 | +
- validate(need(+ #' }) |
||
| 52 | -5x | +||
| 190 | +
- sum(complete_index) > 0 && nrow(x[complete_index, , drop = FALSE]) >= min_nrow,+ #' } |
||
| 53 | -5x | +||
| 191 | +
- paste(c(paste("Number of complete cases is less than:", min_nrow), msg), collapse = "\n")
+ #' if (interactive()) {
|
||
| 54 | +192 |
- ))+ #' shinyApp(ui, server) |
|
| 55 | +193 |
- } else {
+ #' } |
|
| 56 | -10x | +||
| 194 | +
- validate(need(+ validate_has_elements <- function(x, msg) {
|
||
| 57 | -10x | +||
| 195 | +! |
- nrow(x) >= min_nrow,+ validate(need(length(x) > 0, msg)) |
|
| 58 | -10x | +||
| 196 | +
- paste(+ } |
||
| 59 | -10x | +||
| 197 | +
- c(paste("Minimum number of records not met: >=", min_nrow, "records required."), msg),
+
|
||
| 60 | -10x | +||
| 198 | +
- collapse = "\n"+ #' Validates no intersection between two vectors |
||
| 61 | +199 |
- )+ #' |
|
| 62 | +200 |
- ))+ #' `r lifecycle::badge("stable")`
|
|
| 63 | +201 |
- }+ #' |
|
| 64 | +202 |
-
+ #' This function is a wrapper for `shiny::validate`. |
|
| 65 | -10x | +||
| 203 | +
- if (!allow_inf) {
+ #' |
||
| 66 | -6x | +||
| 204 | +
- validate(need(+ #' @param x vector |
||
| 67 | -6x | +||
| 205 | +
- all(vapply(x, function(col) !is.numeric(col) || !any(is.infinite(col)), logical(1))),+ #' @param y vector |
||
| 68 | -6x | +||
| 206 | +
- "Dataframe contains Inf values which is not allowed."+ #' @param msg (`character(1)`) message to display if `x` and `y` intersect |
||
| 69 | +207 |
- ))+ #' |
|
| 70 | +208 |
- }+ #' @export |
|
| 71 | +209 |
- }+ #' |
|
| 72 | +210 |
- }+ #' @examples |
|
| 73 | +211 |
-
+ #' data <- data.frame( |
|
| 74 | +212 |
- #' Validate that dataset has unique rows for key variables+ #' id = c(1:10, 11:20, 1:10), |
|
| 75 | +213 |
- #'+ #' strata = rep(c("A", "B", "C"), each = 10)
|
|
| 76 | +214 |
- #' `r lifecycle::badge("stable")`
+ #' ) |
|
| 77 | +215 |
#' |
|
| 78 | +216 |
- #' This function is a wrapper for `shiny::validate`.+ #' ui <- fluidPage( |
|
| 79 | +217 |
- #'+ #' selectInput("ref1", "Select strata1 to compare",
|
|
| 80 | +218 |
- #' @param x (`data.frame`)+ #' choices = c("A", "B", "C"),
|
|
| 81 | +219 |
- #' @param key (`character`) Vector of ID variables from `x` that identify unique records.+ #' selected = "A" |
|
| 82 | +220 |
- #'+ #' ), |
|
| 83 | +221 |
- #' @export+ #' selectInput("ref2", "Select strata2 to compare",
|
|
| 84 | +222 |
- #'+ #' choices = c("A", "B", "C"),
|
|
| 85 | +223 |
- #' @examples+ #' selected = "B" |
|
| 86 | +224 |
- #' iris$id <- rep(1:50, times = 3)+ #' ), |
|
| 87 | +225 |
- #' ui <- fluidPage(+ #' verbatimTextOutput("summary")
|
|
| 88 | +226 |
- #' selectInput(+ #' ) |
|
| 89 | +227 |
- #' inputId = "species",+ #' |
|
| 90 | +228 |
- #' label = "Select species",+ #' server <- function(input, output) {
|
|
| 91 | +229 |
- #' choices = c("setosa", "versicolor", "virginica"),
+ #' output$summary <- renderText({
|
|
| 92 | +230 |
- #' selected = "setosa",+ #' sample_1 <- data$id[data$strata == input$ref1] |
|
| 93 | +231 |
- #' multiple = TRUE+ #' sample_2 <- data$id[data$strata == input$ref2] |
|
| 94 | +232 |
- #' ),+ #' |
|
| 95 | +233 |
- #' plotOutput("plot")
+ #' validate_no_intersection( |
|
| 96 | +234 |
- #' )+ #' sample_1, sample_2, |
|
| 97 | +235 |
- #' server <- function(input, output) {
+ #' "subjects within strata1 and strata2 cannot overlap" |
|
| 98 | +236 |
- #' output$plot <- renderPlot({
+ #' ) |
|
| 99 | +237 |
- #' iris_f <- iris[iris$Species %in% input$species, ]+ #' paste0( |
|
| 100 | +238 |
- #' validate_one_row_per_id(iris_f, key = c("id"))
+ #' "Number of subject in: reference treatment=", length(sample_1), |
|
| 101 | +239 |
- #'+ #' " comparions treatment=", length(sample_2) |
|
| 102 | +240 |
- #' hist(iris_f$Sepal.Length, breaks = 5)+ #' ) |
|
| 103 | +241 |
#' }) |
|
| 104 | +242 |
#' } |
|
| 105 | +243 |
#' if (interactive()) {
|
|
| 106 | +244 |
#' shinyApp(ui, server) |
|
| 107 | +245 |
#' } |
|
| 108 | +246 |
#' |
|
| 109 | +247 |
- validate_one_row_per_id <- function(x, key = c("USUBJID", "STUDYID")) {
+ validate_no_intersection <- function(x, y, msg) {
|
|
| 110 | +248 | ! |
- validate(need(!any(duplicated(x[key])), paste("Found more than one row per id.")))
+ validate(need(length(intersect(x, y)) == 0, msg)) |
| 111 | +249 |
} |
|
| 112 | +250 | ||
| 113 | +251 |
- #' Validates that vector includes all expected values+ |
|
| 114 | +252 | ++ |
+ #' Validates that dataset contains specific variable+ |
+
| 253 |
#' |
||
| 115 | +254 |
#' `r lifecycle::badge("stable")`
|
|
| 116 | +255 |
#' |
|
| 117 | +256 |
#' This function is a wrapper for `shiny::validate`. |
|
| 118 | +257 |
#' |
|
| 119 | +258 |
- #' @param x Vector of values to test.+ #' @param data (`data.frame`) |
|
| 120 | +259 |
- #' @param choices Vector to test against.+ #' @param varname (`character(1)`) name of variable to check for in `data` |
|
| 121 | +260 |
- #' @param msg (`character(1)`) Error message to display if some elements of `x` are not elements of `choices`.+ #' @param msg (`character(1)`) message to display if `data` does not include `varname` |
|
| 122 | +261 |
#' |
|
| 123 | +262 |
#' @export |
|
| 124 | +263 |
#' |
|
| 125 | +264 |
#' @examples |
|
| 126 | +265 |
- #' ui <- fluidPage(+ #' data <- data.frame( |
|
| 127 | +266 |
- #' selectInput(+ #' one = rep("a", length.out = 20),
|
|
| 128 | +267 |
- #' "species",+ #' two = rep(c("a", "b"), length.out = 20)
|
|
| 129 | +268 |
- #' "Select species",+ #' ) |
|
| 130 | +269 |
- #' choices = c("setosa", "versicolor", "virginica", "unknown species"),
+ #' ui <- fluidPage( |
|
| 131 | +270 |
- #' selected = "setosa",+ #' selectInput( |
|
| 132 | +271 |
- #' multiple = FALSE+ #' "var", |
|
| 133 | +272 | ++ |
+ #' "Select variable",+ |
+
| 273 | ++ |
+ #' choices = c("one", "two", "three", "four"),
+ |
+ |
| 274 | ++ |
+ #' selected = "one"+ |
+ |
| 275 |
#' ), |
||
| 134 | +276 |
#' verbatimTextOutput("summary")
|
|
| 135 | +277 |
#' ) |
|
| 136 | +278 |
#' |
|
| 137 | +279 |
#' server <- function(input, output) {
|
|
| 138 | +280 |
- #' output$summary <- renderPrint({
+ #' output$summary <- renderText({
|
|
| 139 | +281 |
- #' validate_in(input$species, iris$Species, "Species does not exist.")+ #' validate_has_variable(data, input$var) |
|
| 140 | +282 |
- #' nrow(iris[iris$Species == input$species, ])+ #' paste0("Selected treatment variables: ", paste(input$var, collapse = ", "))
|
|
| 141 | +283 |
#' }) |
|
| 142 | +284 |
#' } |
|
| 143 | +285 |
#' if (interactive()) {
|
|
| 144 | +286 |
#' shinyApp(ui, server) |
|
| 145 | +287 |
#' } |
|
| 146 | +288 |
- #'+ validate_has_variable <- function(data, varname, msg) {
+ |
+ |
| 289 | +! | +
+ if (length(varname) != 0) {
+ |
+ |
| 290 | +! | +
+ has_vars <- varname %in% names(data) |
|
| 147 | +291 |
- validate_in <- function(x, choices, msg) {
+
|
|
| 148 | +292 | ! |
- validate(need(length(x) > 0 && length(choices) > 0 && all(x %in% choices), msg))+ if (!all(has_vars)) {
+ |
+
| 293 | +! | +
+ if (missing(msg)) {
+ |
+ |
| 294 | +! | +
+ msg <- sprintf(+ |
+ |
| 295 | +! | +
+ "%s does not have the required variables: %s.",+ |
+ |
| 296 | +! | +
+ deparse(substitute(data)),+ |
+ |
| 297 | +! | +
+ toString(varname[!has_vars]) |
|
| 149 | +298 | ++ |
+ )+ |
+
| 299 | ++ |
+ }+ |
+ |
| 300 | +! | +
+ validate(need(FALSE, msg))+ |
+ |
| 301 | ++ |
+ }+ |
+ |
| 302 | ++ |
+ }+ |
+ |
| 303 |
} |
||
| 150 | +304 | ||
| 151 | +305 |
- #' Validates that vector has length greater than 0+ #' Validate that variables has expected number of levels |
|
| 152 | +306 |
#' |
|
| 153 | +307 |
#' `r lifecycle::badge("stable")`
|
|
| 154 | +308 |
#' |
|
| 155 | +309 | ++ |
+ #' If the number of levels of `x` is less than `min_levels`+ |
+
| 310 | ++ |
+ #' or greater than `max_levels` the validation will fail.+ |
+ |
| 311 |
#' This function is a wrapper for `shiny::validate`. |
||
| 156 | +312 |
#' |
|
| 157 | +313 |
- #' @param x vector+ #' @param x variable name. If `x` is not a factor, the unique values |
|
| 158 | +314 |
- #' @param msg message to display+ #' are treated as levels. |
|
| 159 | +315 |
- #'+ #' @param min_levels cutoff for minimum number of levels of `x` |
|
| 160 | +316 |
- #' @export+ #' @param max_levels cutoff for maximum number of levels of `x` |
|
| 161 | +317 | ++ |
+ #' @param var_name name of variable being validated for use in+ |
+
| 318 | ++ |
+ #' validation message+ |
+ |
| 319 |
#' |
||
| 162 | +320 | ++ |
+ #' @export+ |
+
| 321 |
#' @examples |
||
| 163 | +322 |
#' data <- data.frame( |
|
| 164 | +323 |
- #' id = c(1:10, 11:20, 1:10),+ #' one = rep("a", length.out = 20),
|
|
| 165 | +324 |
- #' strata = rep(c("A", "B"), each = 15)
+ #' two = rep(c("a", "b"), length.out = 20),
|
|
| 166 | +325 | ++ |
+ #' three = rep(c("a", "b", "c"), length.out = 20),
+ |
+
| 326 | ++ |
+ #' four = rep(c("a", "b", "c", "d"), length.out = 20),
+ |
+ |
| 327 | ++ |
+ #' stringsAsFactors = TRUE+ |
+ |
| 328 |
#' ) |
||
| 167 | +329 |
#' ui <- fluidPage( |
|
| 168 | +330 |
- #' selectInput("ref1", "Select strata1 to compare",
+ #' selectInput( |
|
| 169 | +331 |
- #' choices = c("A", "B", "C"), selected = "A"
+ #' "var", |
|
| 170 | +332 |
- #' ),+ #' "Select variable", |
|
| 171 | +333 |
- #' selectInput("ref2", "Select strata2 to compare",
+ #' choices = c("one", "two", "three", "four"),
|
|
| 172 | +334 |
- #' choices = c("A", "B", "C"), selected = "B"
+ #' selected = "one" |
|
| 173 | +335 |
#' ), |
|
| 174 | +336 |
- #' verbatimTextOutput("arm_summary")
+ #' verbatimTextOutput("summary")
|
|
| 175 | +337 |
#' ) |
|
| 176 | +338 |
#' |
|
| 177 | +339 |
#' server <- function(input, output) {
|
|
| 178 | +340 |
- #' output$arm_summary <- renderText({
+ #' output$summary <- renderText({
|
|
| 179 | +341 |
- #' sample_1 <- data$id[data$strata == input$ref1]+ #' validate_n_levels(data[[input$var]], min_levels = 2, max_levels = 15, var_name = input$var) |
|
| 180 | +342 |
- #' sample_2 <- data$id[data$strata == input$ref2]+ #' paste0( |
|
| 181 | +343 |
- #'+ #' "Levels of selected treatment variable: ", |
|
| 182 | +344 |
- #' validate_has_elements(sample_1, "No subjects in strata1.")+ #' paste(levels(data[[input$var]]), |
|
| 183 | +345 |
- #' validate_has_elements(sample_2, "No subjects in strata2.")+ #' collapse = ", " |
|
| 184 | +346 |
- #'+ #' ) |
|
| 185 | +347 |
- #' paste0(+ #' ) |
|
| 186 | +348 |
- #' "Number of samples in: strata1=", length(sample_1),+ #' }) |
|
| 187 | +349 |
- #' " comparions strata2=", length(sample_2)+ #' } |
|
| 188 | +350 |
- #' )+ #' if (interactive()) {
|
|
| 189 | +351 |
- #' })+ #' shinyApp(ui, server) |
|
| 190 | +352 |
#' } |
|
| 191 | +353 |
- #' if (interactive()) {
+ validate_n_levels <- function(x, min_levels = 1, max_levels = 12, var_name) {
|
|
| 192 | -+ | ||
| 354 | +! |
- #' shinyApp(ui, server)+ x_levels <- if (is.factor(x)) {
|
|
| 193 | -+ | ||
| 355 | +! |
- #' }+ levels(x) |
|
| 194 | +356 |
- validate_has_elements <- function(x, msg) {
+ } else {
|
|
| 195 | +357 | ! |
- validate(need(length(x) > 0, msg))+ unique(x) |
| 196 | +358 |
- }+ } |
|
| 197 | +359 | ||
| 198 | -+ | ||
| 360 | +! |
- #' Validates no intersection between two vectors+ if (!is.null(min_levels) && !(is.null(max_levels))) {
|
|
| 199 | -+ | ||
| 361 | +! |
- #'+ validate(need( |
|
| 200 | -+ | ||
| 362 | +! |
- #' `r lifecycle::badge("stable")`
+ length(x_levels) >= min_levels && length(x_levels) <= max_levels, |
|
| 201 | -+ | ||
| 363 | +! |
- #'+ sprintf( |
|
| 202 | -+ | ||
| 364 | +! |
- #' This function is a wrapper for `shiny::validate`.+ "%s variable needs minimum %s level(s) and maximum %s level(s).", |
|
| 203 | -+ | ||
| 365 | +! |
- #'+ var_name, min_levels, max_levels |
|
| 204 | +366 |
- #' @param x vector+ ) |
|
| 205 | +367 |
- #' @param y vector+ )) |
|
| 206 | -+ | ||
| 368 | +! |
- #' @param msg (`character(1)`) message to display if `x` and `y` intersect+ } else if (!is.null(min_levels)) {
|
|
| 207 | -+ | ||
| 369 | +! |
- #'+ validate(need( |
|
| 208 | -+ | ||
| 370 | +! |
- #' @export+ length(x_levels) >= min_levels, |
|
| 209 | -+ | ||
| 371 | +! |
- #'+ sprintf("%s variable needs minimum %s levels(s)", var_name, min_levels)
|
|
| 210 | +372 |
- #' @examples+ )) |
|
| 211 | -+ | ||
| 373 | +! |
- #' data <- data.frame(+ } else if (!is.null(max_levels)) {
|
|
| 212 | -+ | ||
| 374 | +! |
- #' id = c(1:10, 11:20, 1:10),+ validate(need( |
|
| 213 | -+ | ||
| 375 | +! |
- #' strata = rep(c("A", "B", "C"), each = 10)
+ length(x_levels) <= max_levels,+ |
+ |
| 376 | +! | +
+ sprintf("%s variable needs maximum %s level(s)", var_name, max_levels)
|
|
| 214 | +377 |
- #' )+ )) |
|
| 215 | +378 |
- #'+ } |
|
| 216 | +379 |
- #' ui <- fluidPage(+ } |
| 217 | +1 |
- #' selectInput("ref1", "Select strata1 to compare",
+ #' Data summary |
|
| 218 | +2 |
- #' choices = c("A", "B", "C"),
+ #' @description |
|
| 219 | +3 |
- #' selected = "A"+ #' Module and its utils to display the number of rows and subjects in the filtered and unfiltered data. |
|
| 220 | +4 |
- #' ),+ #' |
|
| 221 | +5 |
- #' selectInput("ref2", "Select strata2 to compare",
+ #' @details Handling different data classes: |
|
| 222 | +6 |
- #' choices = c("A", "B", "C"),
+ #' `get_filter_overview()` is a pseudo S3 method which has variants for: |
|
| 223 | +7 |
- #' selected = "B"+ #' - `array` (`data.frame`, `DataFrame`, `array`, `Matrix` and `SummarizedExperiment`): Method variant |
|
| 224 | +8 |
- #' ),+ #' can be applied to any two-dimensional objects on which [ncol()] can be used. |
|
| 225 | +9 |
- #' verbatimTextOutput("summary")
+ #' - `MultiAssayExperiment`: for which summary contains counts for `colData` and all `experiments`. |
|
| 226 | +10 |
- #' )+ #' - For other data types module displays data name with warning icon and no more details. |
|
| 227 | +11 |
#' |
|
| 228 | +12 |
- #' server <- function(input, output) {
+ #' Module includes also "Show/Hide unsupported" button to toggle rows of the summary table |
|
| 229 | +13 |
- #' output$summary <- renderText({
+ #' containing datasets where number of observations are not calculated. |
|
| 230 | +14 |
- #' sample_1 <- data$id[data$strata == input$ref1]+ #' |
|
| 231 | +15 |
- #' sample_2 <- data$id[data$strata == input$ref2]+ #' @param id (`character(1)`) `shiny` module instance id. |
|
| 232 | +16 |
- #'+ #' @param teal_data (`reactive` returning `teal_data`) |
|
| 233 | +17 |
- #' validate_no_intersection(+ #' |
|
| 234 | +18 |
- #' sample_1, sample_2,+ #' @name module_data_summary |
|
| 235 | +19 |
- #' "subjects within strata1 and strata2 cannot overlap"+ #' @rdname module_data_summary |
|
| 236 | +20 |
- #' )+ #' @keywords internal |
|
| 237 | +21 |
- #' paste0(+ #' @return `NULL`. |
|
| 238 | +22 |
- #' "Number of subject in: reference treatment=", length(sample_1),+ NULL |
|
| 239 | +23 |
- #' " comparions treatment=", length(sample_2)+ |
|
| 240 | +24 |
- #' )+ #' @rdname module_data_summary |
|
| 241 | +25 |
- #' })+ ui_data_summary <- function(id) {
|
|
| 242 | -+ | ||
| 26 | +! |
- #' }+ ns <- NS(id) |
|
| 243 | -+ | ||
| 27 | +! |
- #' if (interactive()) {
+ content_id <- ns("filters_overview_contents")
|
|
| 244 | -+ | ||
| 28 | +! |
- #' shinyApp(ui, server)+ tags$div( |
|
| 245 | -+ | ||
| 29 | +! |
- #' }+ id = id, |
|
| 246 | -+ | ||
| 30 | +! |
- #'+ class = "well", |
|
| 247 | -+ | ||
| 31 | +! |
- validate_no_intersection <- function(x, y, msg) {
+ tags$div( |
|
| 248 | +32 | ! |
- validate(need(length(intersect(x, y)) == 0, msg))+ class = "row", |
| 249 | -+ | ||
| 33 | +! |
- }+ tags$div( |
|
| 250 | -+ | ||
| 34 | +! |
-
+ class = "col-sm-9", |
|
| 251 | -+ | ||
| 35 | +! |
-
+ tags$label("Active Filter Summary", class = "text-primary mb-4")
|
|
| 252 | +36 |
- #' Validates that dataset contains specific variable+ ), |
|
| 253 | -+ | ||
| 37 | +! |
- #'+ tags$div( |
|
| 254 | -+ | ||
| 38 | +! |
- #' `r lifecycle::badge("stable")`
+ class = "col-sm-3", |
|
| 255 | -+ | ||
| 39 | +! |
- #'+ tags$i( |
|
| 256 | -+ | ||
| 40 | +! |
- #' This function is a wrapper for `shiny::validate`.+ class = "remove pull-right fa fa-angle-down", |
|
| 257 | -+ | ||
| 41 | +! |
- #'+ style = "cursor: pointer;", |
|
| 258 | -+ | ||
| 42 | +! |
- #' @param data (`data.frame`)+ title = "fold/expand data summary panel", |
|
| 259 | -+ | ||
| 43 | +! |
- #' @param varname (`character(1)`) name of variable to check for in `data`+ onclick = sprintf("togglePanelItems(this, '%s', 'fa-angle-right', 'fa-angle-down');", content_id)
|
|
| 260 | +44 |
- #' @param msg (`character(1)`) message to display if `data` does not include `varname`+ ) |
|
| 261 | +45 |
- #'+ ) |
|
| 262 | +46 |
- #' @export+ ), |
|
| 263 | -+ | ||
| 47 | +! |
- #'+ tags$div( |
|
| 264 | -+ | ||
| 48 | +! | +
+ id = content_id,+ |
+ |
| 49 | +! |
- #' @examples+ tags$div( |
|
| 265 | -+ | ||
| 50 | +! |
- #' data <- data.frame(+ class = "teal_active_summary_filter_panel", |
|
| 266 | -+ | ||
| 51 | +! |
- #' one = rep("a", length.out = 20),
+ tableOutput(ns("table"))
|
|
| 267 | +52 |
- #' two = rep(c("a", "b"), length.out = 20)
+ ) |
|
| 268 | +53 |
- #' )+ ) |
|
| 269 | +54 |
- #' ui <- fluidPage(+ ) |
|
| 270 | +55 |
- #' selectInput(+ } |
|
| 271 | +56 |
- #' "var",+ |
|
| 272 | +57 |
- #' "Select variable",+ #' @rdname module_data_summary |
|
| 273 | +58 |
- #' choices = c("one", "two", "three", "four"),
+ srv_data_summary <- function(id, data) {
|
|
| 274 | -+ | ||
| 59 | +86x |
- #' selected = "one"+ assert_reactive(data) |
|
| 275 | -+ | ||
| 60 | +86x |
- #' ),+ moduleServer( |
|
| 276 | -+ | ||
| 61 | +86x |
- #' verbatimTextOutput("summary")
+ id = id, |
|
| 277 | -+ | ||
| 62 | +86x |
- #' )+ function(input, output, session) {
|
|
| 278 | -+ | ||
| 63 | +86x |
- #'+ logger::log_debug("srv_data_summary initializing")
|
|
| 279 | +64 |
- #' server <- function(input, output) {
+
|
|
| 280 | -+ | ||
| 65 | +86x |
- #' output$summary <- renderText({
+ summary_table <- reactive({
|
|
| 281 | -+ | ||
| 66 | +94x |
- #' validate_has_variable(data, input$var)+ req(inherits(data(), "teal_data")) |
|
| 282 | -+ | ||
| 67 | +88x |
- #' paste0("Selected treatment variables: ", paste(input$var, collapse = ", "))
+ if (!length(data())) {
|
|
| 283 | -+ | ||
| 68 | +! |
- #' })+ return(NULL) |
|
| 284 | +69 |
- #' }+ } |
|
| 285 | -+ | ||
| 70 | +88x |
- #' if (interactive()) {
+ get_filter_overview_wrapper(data) |
|
| 286 | +71 |
- #' shinyApp(ui, server)+ }) |
|
| 287 | +72 |
- #' }+ |
|
| 288 | -+ | ||
| 73 | +86x |
- validate_has_variable <- function(data, varname, msg) {
+ output$table <- renderUI({
|
|
| 289 | -! | +||
| 74 | +94x |
- if (length(varname) != 0) {
+ summary_table_out <- try(summary_table(), silent = TRUE) |
|
| 290 | -! | +||
| 75 | +94x |
- has_vars <- varname %in% names(data)+ if (inherits(summary_table_out, "try-error")) {
|
|
| 291 | +76 | - - | -|
| 292 | -! | -
- if (!all(has_vars)) {
+ # Ignore silent shiny error |
|
| 293 | -! | +||
| 77 | +6x |
- if (missing(msg)) {
+ if (!inherits(attr(summary_table_out, "condition"), "shiny.silent.error")) {
|
|
| 294 | +78 | ! |
- msg <- sprintf(+ stop("Error occurred during data processing. See details in the main panel.")
|
| 295 | -! | +||
| 79 | +
- "%s does not have the required variables: %s.",+ } |
||
| 296 | -! | +||
| 80 | +88x |
- deparse(substitute(data)),+ } else if (is.null(summary_table_out)) {
|
|
| 297 | -! | +||
| 81 | +2x |
- toString(varname[!has_vars])+ "no datasets to show" |
|
| 298 | +82 |
- )+ } else {
|
|
| 299 | -+ | ||
| 83 | +86x |
- }+ is_unsupported <- apply(summary_table(), 1, function(x) all(is.na(x[-1]))) |
|
| 300 | -! | +||
| 84 | +86x |
- validate(need(FALSE, msg))+ summary_table_out[is.na(summary_table_out)] <- "" |
|
| 301 | -+ | ||
| 85 | +86x |
- }+ body_html <- apply( |
|
| 302 | -+ | ||
| 86 | +86x |
- }+ summary_table_out, |
|
| 303 | -+ | ||
| 87 | +86x |
- }+ 1, |
|
| 304 | -+ | ||
| 88 | +86x |
-
+ function(x) {
|
|
| 305 | -+ | ||
| 89 | +162x |
- #' Validate that variables has expected number of levels+ is_supported <- !all(x[-1] == "") |
|
| 306 | -+ | ||
| 90 | +162x |
- #'+ if (is_supported) {
|
|
| 307 | -+ | ||
| 91 | +153x |
- #' `r lifecycle::badge("stable")`
+ tags$tr( |
|
| 308 | -+ | ||
| 92 | +153x |
- #'+ tagList( |
|
| 309 | -+ | ||
| 93 | +153x |
- #' If the number of levels of `x` is less than `min_levels`+ tags$td(x[1]), |
|
| 310 | -+ | ||
| 94 | +153x |
- #' or greater than `max_levels` the validation will fail.+ lapply(x[-1], tags$td) |
|
| 311 | +95 |
- #' This function is a wrapper for `shiny::validate`.+ ) |
|
| 312 | +96 |
- #'+ ) |
|
| 313 | +97 |
- #' @param x variable name. If `x` is not a factor, the unique values+ } |
|
| 314 | +98 |
- #' are treated as levels.+ } |
|
| 315 | +99 |
- #' @param min_levels cutoff for minimum number of levels of `x`+ ) |
|
| 316 | +100 |
- #' @param max_levels cutoff for maximum number of levels of `x`+ |
|
| 317 | -+ | ||
| 101 | +86x |
- #' @param var_name name of variable being validated for use in+ header_labels <- tools::toTitleCase(names(summary_table_out)) |
|
| 318 | -+ | ||
| 102 | +86x |
- #' validation message+ header_labels[header_labels == "Dataname"] <- "Data Name" |
|
| 319 | -+ | ||
| 103 | +86x |
- #'+ header_html <- tags$tr(tagList(lapply(header_labels, tags$td))) |
|
| 320 | +104 |
- #' @export+ |
|
| 321 | -+ | ||
| 105 | +86x |
- #' @examples+ table_html <- tags$table( |
|
| 322 | -+ | ||
| 106 | +86x |
- #' data <- data.frame(+ class = "table custom-table", |
|
| 323 | -+ | ||
| 107 | +86x |
- #' one = rep("a", length.out = 20),
+ tags$thead(header_html), |
|
| 324 | -+ | ||
| 108 | +86x |
- #' two = rep(c("a", "b"), length.out = 20),
+ tags$tbody(body_html) |
|
| 325 | +109 |
- #' three = rep(c("a", "b", "c"), length.out = 20),
+ ) |
|
| 326 | -+ | ||
| 110 | +86x |
- #' four = rep(c("a", "b", "c", "d"), length.out = 20),
+ div( |
|
| 327 | -+ | ||
| 111 | +86x |
- #' stringsAsFactors = TRUE+ table_html, |
|
| 328 | -+ | ||
| 112 | +86x |
- #' )+ if (any(is_unsupported)) {
|
|
| 329 | -+ | ||
| 113 | +9x |
- #' ui <- fluidPage(+ p( |
|
| 330 | -+ | ||
| 114 | +9x |
- #' selectInput(+ class = c("pull-right", "float-right", "text-secondary"),
|
|
| 331 | -+ | ||
| 115 | +9x |
- #' "var",+ style = "font-size: 0.8em;", |
|
| 332 | -+ | ||
| 116 | +9x |
- #' "Select variable",+ sprintf("And %s more unfilterable object(s)", sum(is_unsupported)),
|
|
| 333 | -+ | ||
| 117 | +9x |
- #' choices = c("one", "two", "three", "four"),
+ icon( |
|
| 334 | -+ | ||
| 118 | +9x |
- #' selected = "one"+ name = "far fa-circle-question", |
|
| 335 | -+ | ||
| 119 | +9x |
- #' ),+ title = paste( |
|
| 336 | -+ | ||
| 120 | +9x |
- #' verbatimTextOutput("summary")
+ sep = "", |
|
| 337 | -+ | ||
| 121 | +9x |
- #' )+ collapse = "\n", |
|
| 338 | -+ | ||
| 122 | +9x |
- #'+ shQuote(summary_table()[is_unsupported, "dataname"]), |
|
| 339 | +123 |
- #' server <- function(input, output) {
+ " (",
|
|
| 340 | -+ | ||
| 124 | +9x |
- #' output$summary <- renderText({
+ vapply( |
|
| 341 | -+ | ||
| 125 | +9x |
- #' validate_n_levels(data[[input$var]], min_levels = 2, max_levels = 15, var_name = input$var)+ summary_table()[is_unsupported, "dataname"], |
|
| 342 | -+ | ||
| 126 | +9x |
- #' paste0(+ function(x) class(data()[[x]])[1], |
|
| 343 | -+ | ||
| 127 | +9x |
- #' "Levels of selected treatment variable: ",+ character(1L) |
|
| 344 | +128 |
- #' paste(levels(data[[input$var]]),+ ), |
|
| 345 | +129 |
- #' collapse = ", "+ ")" |
|
| 346 | +130 |
- #' )+ ) |
|
| 347 | +131 |
- #' )+ ) |
|
| 348 | +132 |
- #' })+ ) |
|
| 349 | +133 |
- #' }+ } |
|
| 350 | +134 |
- #' if (interactive()) {
+ ) |
|
| 351 | +135 |
- #' shinyApp(ui, server)+ } |
|
| 352 | +136 |
- #' }+ }) |
|
| 353 | +137 |
- validate_n_levels <- function(x, min_levels = 1, max_levels = 12, var_name) {
- |
- |
| 354 | -! | -
- x_levels <- if (is.factor(x)) {
+
|
|
| 355 | -! | +||
| 138 | +86x |
- levels(x)+ NULL |
|
| 356 | +139 |
- } else {
+ } |
|
| 357 | -! | +||
| 140 | +
- unique(x)+ ) |
||
| 358 | +141 |
- }+ } |
|
| 359 | +142 | ||
| 360 | -! | -
- if (!is.null(min_levels) && !(is.null(max_levels))) {
- |
- |
| 361 | -! | -
- validate(need(- |
- |
| 362 | -! | +||
| 143 | +
- length(x_levels) >= min_levels && length(x_levels) <= max_levels,+ #' @rdname module_data_summary |
||
| 363 | -! | +||
| 144 | +
- sprintf(+ get_filter_overview_wrapper <- function(teal_data) {
|
||
| 364 | -! | +||
| 145 | +
- "%s variable needs minimum %s level(s) and maximum %s level(s).",+ # Sort datanames in topological order |
||
| 365 | -! | +||
| 146 | +88x |
- var_name, min_levels, max_levels+ datanames <- names(teal_data()) |
|
| 366 | -+ | ||
| 147 | +88x |
- )+ joinkeys <- teal.data::join_keys(teal_data()) |
|
| 367 | +148 |
- ))+ |
|
| 368 | -! | +||
| 149 | +88x |
- } else if (!is.null(min_levels)) {
+ current_data_objs <- sapply( |
|
| 369 | -! | +||
| 150 | +88x |
- validate(need(+ datanames, |
|
| 370 | -! | +||
| 151 | +88x |
- length(x_levels) >= min_levels,+ function(name) teal_data()[[name]], |
|
| 371 | -! | +||
| 152 | +88x |
- sprintf("%s variable needs minimum %s levels(s)", var_name, min_levels)
+ simplify = FALSE |
|
| 372 | +153 |
- ))- |
- |
| 373 | -! | -
- } else if (!is.null(max_levels)) {
+ ) |
|
| 374 | -! | +||
| 154 | +88x |
- validate(need(+ initial_data_objs <- teal_data()[[".raw_data"]] |
|
| 375 | -! | +||
| 155 | +
- length(x_levels) <= max_levels,+ |
||
| 376 | -! | +||
| 156 | +88x |
- sprintf("%s variable needs maximum %s level(s)", var_name, max_levels)
+ out <- lapply( |
|
| 377 | -+ | ||
| 157 | +88x |
- ))+ datanames, |
|
| 378 | -+ | ||
| 158 | +88x |
- }+ function(dataname) {
|
|
| 379 | -+ | ||
| 159 | +157x |
- }+ parent <- teal.data::parent(joinkeys, dataname) |
| 1 | -+ | |||
| 160 | +157x |
- #' Data summary+ subject_keys <- if (length(parent) > 0) {
|
||
| 2 | -+ | |||
| 161 | +8x |
- #' @description+ names(joinkeys[dataname, parent]) |
||
| 3 | +162 |
- #' Module and its utils to display the number of rows and subjects in the filtered and unfiltered data.+ } else {
|
||
| 4 | -+ | |||
| 163 | +149x |
- #'+ joinkeys[dataname, dataname] |
||
| 5 | +164 |
- #' @details Handling different data classes:+ } |
||
| 6 | -+ | |||
| 165 | +157x |
- #' `get_filter_overview()` is a pseudo S3 method which has variants for:+ get_filter_overview( |
||
| 7 | -+ | |||
| 166 | +157x |
- #' - `array` (`data.frame`, `DataFrame`, `array`, `Matrix` and `SummarizedExperiment`): Method variant+ current_data = current_data_objs[[dataname]], |
||
| 8 | -+ | |||
| 167 | +157x |
- #' can be applied to any two-dimensional objects on which [ncol()] can be used.+ initial_data = initial_data_objs[[dataname]], |
||
| 9 | -+ | |||
| 168 | +157x |
- #' - `MultiAssayExperiment`: for which summary contains counts for `colData` and all `experiments`.+ dataname = dataname, |
||
| 10 | -+ | |||
| 169 | +157x |
- #' - For other data types module displays data name with warning icon and no more details.+ subject_keys = subject_keys |
||
| 11 | +170 |
- #'+ ) |
||
| 12 | +171 |
- #' Module includes also "Show/Hide unsupported" button to toggle rows of the summary table+ } |
||
| 13 | +172 |
- #' containing datasets where number of observations are not calculated.+ ) |
||
| 14 | +173 |
- #'+ |
||
| 15 | -+ | |||
| 174 | +88x |
- #' @param id (`character(1)`) `shiny` module instance id.+ do.call(.smart_rbind, out) |
||
| 16 | +175 |
- #' @param teal_data (`reactive` returning `teal_data`)+ } |
||
| 17 | +176 |
- #'+ |
||
| 18 | +177 |
- #' @name module_data_summary+ |
||
| 19 | +178 |
#' @rdname module_data_summary |
||
| 20 | -- |
- #' @keywords internal- |
- ||
| 21 | +179 |
- #' @return `NULL`.+ #' @param current_data (`object`) current object (after filtering and transforming). |
||
| 22 | +180 |
- NULL+ #' @param initial_data (`object`) initial object. |
||
| 23 | +181 |
-
+ #' @param dataname (`character(1)`) |
||
| 24 | +182 |
- #' @rdname module_data_summary+ #' @param subject_keys (`character`) names of the columns which determine a single unique subjects |
||
| 25 | +183 |
- ui_data_summary <- function(id) {
- |
- ||
| 26 | -! | -
- ns <- NS(id)- |
- ||
| 27 | -! | -
- content_id <- ns("filters_overview_contents")
- |
- ||
| 28 | -! | -
- tags$div(- |
- ||
| 29 | -! | -
- id = id,- |
- ||
| 30 | -! | -
- class = "well",- |
- ||
| 31 | -! | -
- tags$div(+ get_filter_overview <- function(current_data, initial_data, dataname, subject_keys) {
|
||
| 32 | -! | +|||
| 184 | +162x |
- class = "row",+ if (inherits(current_data, c("data.frame", "DataFrame", "array", "Matrix", "SummarizedExperiment"))) {
|
||
| 33 | -! | +|||
| 185 | +152x |
- tags$div(+ get_filter_overview_array(current_data, initial_data, dataname, subject_keys) |
||
| 34 | -! | +|||
| 186 | +10x |
- class = "col-sm-9",+ } else if (inherits(current_data, "MultiAssayExperiment")) {
|
||
| 35 | -! | +|||
| 187 | +1x |
- tags$label("Active Filter Summary", class = "text-primary mb-4")
+ get_filter_overview_MultiAssayExperiment(current_data, initial_data, dataname) |
||
| 36 | +188 |
- ),- |
- ||
| 37 | -! | -
- tags$div(- |
- ||
| 38 | -! | -
- class = "col-sm-3",- |
- ||
| 39 | -! | -
- tags$i(+ } else {
|
||
| 40 | -! | +|||
| 189 | +9x |
- class = "remove pull-right fa fa-angle-down",+ data.frame(dataname = dataname) |
||
| 41 | -! | +|||
| 190 | +
- style = "cursor: pointer;",+ } |
|||
| 42 | -! | +|||
| 191 | +
- title = "fold/expand data summary panel",+ } |
|||
| 43 | -! | +|||
| 192 | +
- onclick = sprintf("togglePanelItems(this, '%s', 'fa-angle-right', 'fa-angle-down');", content_id)
+
|
|||
| 44 | +193 |
- )+ #' @rdname module_data_summary |
||
| 45 | +194 |
- )+ get_filter_overview_array <- function(current_data, |
||
| 46 | +195 |
- ),+ initial_data, |
||
| 47 | -! | +|||
| 196 | +
- tags$div(+ dataname, |
|||
| 48 | -! | +|||
| 197 | +
- id = content_id,+ subject_keys) {
|
|||
| 49 | -! | +|||
| 198 | +152x |
- tags$div(+ if (length(subject_keys) == 0) {
|
||
| 50 | -! | +|||
| 199 | +138x |
- class = "teal_active_summary_filter_panel",+ data.frame( |
||
| 51 | -! | +|||
| 200 | +138x |
- tableOutput(ns("table"))
+ dataname = dataname, |
||
| 52 | -+ | |||
| 201 | +138x |
- )+ obs = if (!is.null(initial_data)) {
|
||
| 53 | -+ | |||
| 202 | +127x |
- )+ sprintf("%s/%s", nrow(current_data), nrow(initial_data))
|
||
| 54 | +203 |
- )+ } else {
|
||
| 55 | -+ | |||
| 204 | +11x |
- }+ nrow(current_data) |
||
| 56 | +205 |
-
+ } |
||
| 57 | +206 |
- #' @rdname module_data_summary+ ) |
||
| 58 | +207 |
- srv_data_summary <- function(id, teal_data) {
+ } else {
|
||
| 59 | -86x | +208 | +14x |
- assert_reactive(teal_data)+ data.frame( |
| 60 | -86x | +209 | +14x |
- moduleServer(+ dataname = dataname, |
| 61 | -86x | +210 | +14x |
- id = id,+ obs = if (!is.null(initial_data)) {
|
| 62 | -86x | +211 | +13x |
- function(input, output, session) {
+ sprintf("%s/%s", nrow(current_data), nrow(initial_data))
+ |
+
| 212 | ++ |
+ } else {
|
||
| 63 | -86x | +213 | +1x |
- logger::log_debug("srv_data_summary initializing")
+ nrow(current_data) |
| 64 | +214 |
-
+ }, |
||
| 65 | -86x | +215 | +14x |
- summary_table <- reactive({
+ subjects = if (!is.null(initial_data)) {
|
| 66 | -94x | +216 | +13x | +
+ sprintf("%s/%s", nrow(unique(current_data[subject_keys])), nrow(unique(initial_data[subject_keys])))
+ |
+
| 217 | +
- req(inherits(teal_data(), "teal_data"))+ } else {
|
|||
| 67 | -88x | +218 | +1x |
- if (!length(teal_data())) {
+ nrow(unique(current_data[subject_keys])) |
| 68 | -! | +|||
| 219 | +
- return(NULL)+ } |
|||
| 69 | +220 |
- }+ ) |
||
| 70 | -88x | +|||
| 221 | +
- get_filter_overview_wrapper(teal_data)+ } |
|||
| 71 | +222 |
- })+ } |
||
| 72 | +223 | |||
| 73 | -86x | +|||
| 224 | +
- output$table <- renderUI({
+ #' @rdname module_data_summary |
|||
| 74 | -94x | +|||
| 225 | +
- summary_table_out <- try(summary_table(), silent = TRUE)+ get_filter_overview_MultiAssayExperiment <- function(current_data, # nolint: object_length, object_name. |
|||
| 75 | -94x | +|||
| 226 | +
- if (inherits(summary_table_out, "try-error")) {
+ initial_data, |
|||
| 76 | +227 |
- # Ignore silent shiny error+ dataname) {
|
||
| 77 | -6x | +228 | +1x |
- if (!inherits(attr(summary_table_out, "condition"), "shiny.silent.error")) {
+ experiment_names <- names(current_data) |
| 78 | -! | +|||
| 229 | +1x |
- stop("Error occurred during data processing. See details in the main panel.")
+ mae_info <- data.frame( |
||
| 79 | -+ | |||
| 230 | +1x |
- }+ dataname = dataname, |
||
| 80 | -88x | +231 | +1x |
- } else if (is.null(summary_table_out)) {
+ subjects = if (!is.null(initial_data)) {
|
| 81 | -2x | +|||
| 232 | +! |
- "no datasets to show"+ sprintf("%s/%s", nrow(current_data@colData), nrow(initial_data@colData))
|
||
| 82 | +233 |
- } else {
+ } else {
|
||
| 83 | -86x | +234 | +1x |
- is_unsupported <- apply(summary_table(), 1, function(x) all(is.na(x[-1])))+ nrow(current_data@colData) |
| 84 | -86x | +|||
| 235 | +
- summary_table_out[is.na(summary_table_out)] <- ""+ } |
|||
| 85 | -86x | +|||
| 236 | +
- body_html <- apply(+ )+ |
+ |||
| 237 | ++ | + | ||
| 86 | -86x | +238 | +1x |
- summary_table_out,+ experiment_obs_info <- do.call("rbind", lapply(
|
| 87 | -86x | +239 | +1x |
- 1,+ experiment_names, |
| 88 | -86x | +240 | +1x |
- function(x) {
+ function(experiment_name) {
|
| 89 | -162x | +241 | +5x |
- is_supported <- !all(x[-1] == "")+ transform( |
| 90 | -162x | +242 | +5x |
- if (is_supported) {
+ get_filter_overview( |
| 91 | -153x | +243 | +5x |
- tags$tr(+ current_data[[experiment_name]], |
| 92 | -153x | +244 | +5x |
- tagList(+ initial_data[[experiment_name]], |
| 93 | -153x | +245 | +5x |
- tags$td(x[1]),+ dataname = experiment_name, |
| 94 | -153x | +246 | +5x |
- lapply(x[-1], tags$td)+ subject_keys = join_keys() # empty join keys |
| 95 | +247 |
- )+ ), |
||
| 96 | -+ | |||
| 248 | +5x |
- )+ dataname = paste0(" - ", experiment_name)
|
||
| 97 | +249 |
- }+ ) |
||
| 98 | +250 |
- }+ } |
||
| 99 | +251 |
- )+ )) |
||
| 100 | +252 | |||
| 101 | -86x | +253 | +1x |
- header_labels <- tools::toTitleCase(names(summary_table_out))+ get_experiment_keys <- function(mae, experiment) {
|
| 102 | -86x | +254 | +5x |
- header_labels[header_labels == "Dataname"] <- "Data Name"+ sample_subset <- mae@sampleMap[mae@sampleMap$colname %in% colnames(experiment), ] |
| 103 | -86x | +255 | +5x |
- header_html <- tags$tr(tagList(lapply(header_labels, tags$td)))+ length(unique(sample_subset$primary)) |
| 104 | +256 | - - | -||
| 105 | -86x | -
- table_html <- tags$table(- |
- ||
| 106 | -86x | -
- class = "table custom-table",+ } |
||
| 107 | -86x | +|||
| 257 | +
- tags$thead(header_html),+ |
|||
| 108 | -86x | -
- tags$tbody(body_html)- |
- ||
| 109 | -+ | 258 | +1x |
- )+ experiment_subjects_info <- do.call("rbind", lapply(
|
| 110 | -86x | +259 | +1x |
- div(+ experiment_names, |
| 111 | -86x | +260 | +1x |
- table_html,+ function(experiment_name) {
|
| 112 | -86x | +261 | +5x |
- if (any(is_unsupported)) {
+ data.frame( |
| 113 | -9x | +262 | +5x |
- p(+ subjects = if (!is.null(initial_data)) {
|
| 114 | -9x | +|||
| 263 | +! |
- class = c("pull-right", "float-right", "text-secondary"),
+ sprintf( |
||
| 115 | -9x | +|||
| 264 | +! |
- style = "font-size: 0.8em;",+ "%s/%s", |
||
| 116 | -9x | +|||
| 265 | +! |
- sprintf("And %s more unfilterable object(s)", sum(is_unsupported)),
+ get_experiment_keys(current_data, current_data[[experiment_name]]), |
||
| 117 | -9x | +|||
| 266 | +! |
- icon(+ get_experiment_keys(current_data, initial_data[[experiment_name]]) |
||
| 118 | -9x | +|||
| 267 | +
- name = "far fa-circle-question",+ ) |
|||
| 119 | -9x | +|||
| 268 | +
- title = paste(+ } else {
|
|||
| 120 | -9x | +269 | +5x |
- sep = "",+ get_experiment_keys(current_data, current_data[[experiment_name]]) |
| 121 | -9x | +|||
| 270 | +
- collapse = "\n",+ } |
|||
| 122 | -9x | +|||
| 271 | +
- shQuote(summary_table()[is_unsupported, "dataname"]),+ ) |
|||
| 123 | +272 |
- " (",
+ } |
||
| 124 | -9x | +|||
| 273 | +
- vapply(+ )) |
|||
| 125 | -9x | +|||
| 274 | +
- summary_table()[is_unsupported, "dataname"],+ |
|||
| 126 | -9x | +275 | +1x |
- function(x) class(teal_data()[[x]])[1],+ experiment_info <- cbind(experiment_obs_info, experiment_subjects_info) |
| 127 | -9x | +276 | +1x |
- character(1L)+ .smart_rbind(mae_info, experiment_info) |
| 128 | +277 |
- ),+ } |
| 129 | +1 |
- ")"+ #' Filter panel module in teal |
||
| 130 | +2 |
- )+ #' |
||
| 131 | +3 |
- )+ #' Creates filter panel module from `teal_data` object and returns `teal_data`. It is build in a way |
||
| 132 | +4 |
- )+ #' that filter panel changes and anything what happens before (e.g. [`module_init_data`]) is triggering |
||
| 133 | +5 |
- }+ #' further reactive events only if something has changed and if the module is visible. Thanks to |
||
| 134 | +6 |
- )+ #' this special implementation all modules' data are recalculated only for those modules which are |
||
| 135 | +7 |
- }+ #' currently displayed. |
||
| 136 | +8 |
- })+ #' |
||
| 137 | +9 | - - | -||
| 138 | -86x | -
- NULL+ #' @return A `eventReactive` containing `teal_data` containing filtered objects and filter code. |
||
| 139 | +10 |
- }+ #' `eventReactive` triggers only if all conditions are met: |
||
| 140 | +11 |
- )+ #' - tab is selected (`is_active`) |
||
| 141 | +12 |
- }+ #' - when filters are changed (`get_filter_expr` is different than previous) |
||
| 142 | +13 |
-
+ #' |
||
| 143 | +14 |
- #' @rdname module_data_summary+ #' @inheritParams module_teal_module |
||
| 144 | +15 |
- get_filter_overview_wrapper <- function(teal_data) {
+ #' @param active_datanames (`reactive` returning `character`) this module's data names |
||
| 145 | +16 |
- # Sort datanames in topological order+ #' @name module_filter_data |
||
| 146 | -88x | +|||
| 17 | +
- datanames <- names(teal_data())+ #' @keywords internal |
|||
| 147 | -88x | +|||
| 18 | +
- joinkeys <- teal.data::join_keys(teal_data())+ NULL |
|||
| 148 | +19 | |||
| 149 | -88x | +|||
| 20 | +
- current_data_objs <- sapply(+ #' @rdname module_filter_data |
|||
| 150 | -88x | +|||
| 21 | +
- datanames,+ ui_filter_data <- function(id) {
|
|||
| 151 | -88x | +|||
| 22 | +! |
- function(name) teal_data()[[name]],+ ns <- shiny::NS(id) |
||
| 152 | -88x | +|||
| 23 | +! |
- simplify = FALSE+ uiOutput(ns("panel"))
|
||
| 153 | +24 |
- )+ } |
||
| 154 | -88x | +|||
| 25 | +
- initial_data_objs <- teal_data()[[".raw_data"]]+ |
|||
| 155 | +26 |
-
+ #' @rdname module_filter_data |
||
| 156 | -88x | +|||
| 27 | +
- out <- lapply(+ srv_filter_data <- function(id, datasets, active_datanames, data, is_active) {
|
|||
| 157 | -88x | +28 | +86x |
- datanames,+ assert_reactive(datasets) |
| 158 | -88x | +29 | +86x |
- function(dataname) {
+ moduleServer(id, function(input, output, session) {
|
| 159 | -157x | +30 | +86x |
- parent <- teal.data::parent(joinkeys, dataname)+ active_corrected <- reactive(intersect(active_datanames(), datasets()$datanames())) |
| 160 | -157x | +|||
| 31 | +
- subject_keys <- if (length(parent) > 0) {
+
|
|||
| 161 | -8x | +32 | +86x |
- names(joinkeys[dataname, parent])+ output$panel <- renderUI({
|
| 162 | -+ | |||
| 33 | +88x |
- } else {
+ req(inherits(datasets(), "FilteredData")) |
||
| 163 | -149x | +34 | +88x |
- joinkeys[dataname, dataname]+ isolate({
|
| 164 | +35 |
- }+ # render will be triggered only when FilteredData object changes (not when filters change) |
||
| 165 | -157x | +|||
| 36 | +
- get_filter_overview(+ # technically it means that teal_data_module needs to be refreshed |
|||
| 166 | -157x | +37 | +88x |
- current_data = current_data_objs[[dataname]],+ logger::log_debug("srv_filter_panel rendering filter panel.")
|
| 167 | -157x | +38 | +88x |
- initial_data = initial_data_objs[[dataname]],+ if (length(active_corrected())) {
|
| 168 | -157x | +39 | +86x |
- dataname = dataname,+ datasets()$srv_active("filters", active_datanames = active_corrected)
|
| 169 | -157x | +40 | +86x |
- subject_keys = subject_keys+ datasets()$ui_active(session$ns("filters"), active_datanames = active_corrected)
|
| 170 | +41 |
- )+ } |
||
| 171 | +42 |
- }+ }) |
||
| 172 | +43 |
- )+ }) |
||
| 173 | +44 | |||
| 174 | -88x | +45 | +86x |
- do.call(.smart_rbind, out)+ trigger_data <- .observe_active_filter_changed(datasets, is_active, active_corrected, data) |
| 175 | +46 |
- }+ |
||
| 176 | -+ | |||
| 47 | +86x |
-
+ eventReactive(trigger_data(), {
|
||
| 177 | -+ | |||
| 48 | +89x |
-
+ .make_filtered_teal_data(modules, data = data(), datasets = datasets(), datanames = active_corrected()) |
||
| 178 | +49 |
- #' @rdname module_data_summary+ }) |
||
| 179 | +50 |
- #' @param current_data (`object`) current object (after filtering and transforming).+ }) |
||
| 180 | +51 |
- #' @param initial_data (`object`) initial object.+ } |
||
| 181 | +52 |
- #' @param dataname (`character(1)`)+ |
||
| 182 | +53 |
- #' @param subject_keys (`character`) names of the columns which determine a single unique subjects+ #' @rdname module_filter_data |
||
| 183 | +54 |
- get_filter_overview <- function(current_data, initial_data, dataname, subject_keys) {
+ .make_filtered_teal_data <- function(modules, data, datasets = NULL, datanames) {
|
||
| 184 | -162x | +55 | +89x |
- if (inherits(current_data, c("data.frame", "DataFrame", "array", "Matrix", "SummarizedExperiment"))) {
+ data <- eval_code( |
| 185 | -152x | +56 | +89x |
- get_filter_overview_array(current_data, initial_data, dataname, subject_keys)+ data, |
| 186 | -10x | +57 | +89x |
- } else if (inherits(current_data, "MultiAssayExperiment")) {
+ paste0( |
| 187 | -1x | +58 | +89x |
- get_filter_overview_MultiAssayExperiment(current_data, initial_data, dataname)+ ".raw_data <- list2env(list(",
|
| 188 | -+ | |||
| 59 | +89x |
- } else {
+ toString(sprintf("%1$s = %1$s", sapply(datanames, as.name))),
|
||
| 189 | -9x | +60 | +89x |
- data.frame(dataname = dataname)+ "))\n", |
| 190 | -+ | |||
| 61 | +89x |
- }+ "lockEnvironment(.raw_data) # @linksto .raw_data" # this is environment and it is shared by qenvs. CAN'T MODIFY! |
||
| 191 | +62 |
- }+ ) |
||
| 192 | +63 |
-
+ ) |
||
| 193 | -+ | |||
| 64 | +89x |
- #' @rdname module_data_summary+ filtered_code <- .get_filter_expr(datasets = datasets, datanames = datanames)+ |
+ ||
| 65 | +89x | +
+ filtered_teal_data <- .append_evaluated_code(data, filtered_code)+ |
+ ||
| 66 | +89x | +
+ filtered_datasets <- sapply(datanames, function(x) datasets$get_data(x, filtered = TRUE), simplify = FALSE)+ |
+ ||
| 67 | +89x | +
+ filtered_teal_data <- .append_modified_data(filtered_teal_data, filtered_datasets)+ |
+ ||
| 68 | +89x | +
+ filtered_teal_data |
||
| 194 | +69 |
- get_filter_overview_array <- function(current_data,+ } |
||
| 195 | +70 |
- initial_data,+ |
||
| 196 | +71 |
- dataname,+ #' @rdname module_filter_data |
||
| 197 | +72 |
- subject_keys) {
+ .observe_active_filter_changed <- function(datasets, is_active, active_datanames, data) {
|
||
| 198 | -152x | +73 | +86x |
- if (length(subject_keys) == 0) {
+ previous_signature <- reactiveVal(NULL) |
| 199 | -138x | +74 | +86x |
- data.frame(+ filter_changed <- reactive({
|
| 200 | -138x | +75 | +195x |
- dataname = dataname,+ req(inherits(datasets(), "FilteredData")) |
| 201 | -138x | +76 | +195x |
- obs = if (!is.null(initial_data)) {
+ new_signature <- c( |
| 202 | -127x | +77 | +195x |
- sprintf("%s/%s", nrow(current_data), nrow(initial_data))
+ teal.code::get_code(data()),+ |
+
| 78 | +195x | +
+ .get_filter_expr(datasets = datasets(), datanames = active_datanames()) |
||
| 203 | +79 |
- } else {
+ ) |
||
| 204 | -11x | +80 | +195x |
- nrow(current_data)+ if (!identical(previous_signature(), new_signature)) {
+ |
+
| 81 | +94x | +
+ previous_signature(new_signature)+ |
+ ||
| 82 | +94x | +
+ TRUE+ |
+ ||
| 83 | ++ |
+ } else {
+ |
+ ||
| 84 | +101x | +
+ FALSE |
||
| 205 | +85 |
- }+ } |
||
| 206 | +86 |
- )+ }) |
||
| 207 | +87 |
- } else {
- |
- ||
| 208 | -14x | -
- data.frame(+ |
||
| 209 | -14x | +88 | +86x |
- dataname = dataname,+ trigger_data <- reactiveVal(NULL) |
| 210 | -14x | +89 | +86x |
- obs = if (!is.null(initial_data)) {
+ observe({
|
| 211 | -13x | -
- sprintf("%s/%s", nrow(current_data), nrow(initial_data))
- |
- ||
| 212 | -+ | 90 | +208x |
- } else {
+ if (isTRUE(is_active() && filter_changed())) {
|
| 213 | -1x | -
- nrow(current_data)- |
- ||
| 214 | -+ | 91 | +94x |
- },+ isolate({
|
| 215 | -14x | +92 | +94x |
- subjects = if (!is.null(initial_data)) {
+ if (is.null(trigger_data())) {
|
| 216 | -13x | +93 | +86x |
- sprintf("%s/%s", nrow(unique(current_data[subject_keys])), nrow(unique(initial_data[subject_keys])))
+ trigger_data(0) |
| 217 | +94 |
- } else {
+ } else {
|
||
| 218 | -1x | +95 | +8x |
- nrow(unique(current_data[subject_keys]))+ trigger_data(trigger_data() + 1) |
| 219 | +96 |
- }+ } |
||
| 220 | +97 |
- )+ }) |
||
| 221 | +98 |
- }+ } |
||
| 222 | +99 |
- }+ }) |
||
| 223 | +100 | |||
| 224 | -+ | |||
| 101 | +86x |
- #' @rdname module_data_summary+ trigger_data |
||
| 225 | +102 |
- get_filter_overview_MultiAssayExperiment <- function(current_data, # nolint: object_length, object_name.+ } |
||
| 226 | +103 |
- initial_data,+ |
||
| 227 | +104 |
- dataname) {
- |
- ||
| 228 | -1x | -
- experiment_names <- names(current_data)+ #' @rdname module_filter_data |
||
| 229 | -1x | +|||
| 105 | +
- mae_info <- data.frame(+ .get_filter_expr <- function(datasets, datanames) {
|
|||
| 230 | -1x | +106 | +284x |
- dataname = dataname,+ if (length(datanames)) {
|
| 231 | -1x | -
- subjects = if (!is.null(initial_data)) {
- |
- ||
| 232 | -! | +107 | +278x |
- sprintf("%s/%s", nrow(current_data@colData), nrow(initial_data@colData))
+ teal.slice::get_filter_expr(datasets = datasets, datanames = datanames) |
| 233 | +108 |
- } else {
+ } else {
|
||
| 234 | -1x | +109 | +6x |
- nrow(current_data@colData)+ NULL |
| 235 | +110 |
- }+ } |
||
| 236 | +111 |
- )+ } |
| 237 | +1 | - - | -|
| 238 | -1x | -
- experiment_obs_info <- do.call("rbind", lapply(
- |
- |
| 239 | -1x | -
- experiment_names,- |
- |
| 240 | -1x | -
- function(experiment_name) {
- |
- |
| 241 | -5x | -
- transform(- |
- |
| 242 | -5x | -
- get_filter_overview(- |
- |
| 243 | -5x | -
- current_data[[experiment_name]],+ #' Data module for `teal` applications |
|
| 244 | -5x | +||
| 2 | +
- initial_data[[experiment_name]],+ #' |
||
| 245 | -5x | +||
| 3 | +
- dataname = experiment_name,+ #' @description |
||
| 246 | -5x | +||
| 4 | +
- subject_keys = join_keys() # empty join keys+ #' `r lifecycle::badge("experimental")`
|
||
| 247 | +5 |
- ),+ #' |
|
| 248 | -5x | +||
| 6 | +
- dataname = paste0(" - ", experiment_name)
+ #' Create a `teal_data_module` object and evaluate code on it with history tracking. |
||
| 249 | +7 |
- )+ #' |
|
| 250 | +8 |
- }+ #' @details |
|
| 251 | +9 |
- ))+ #' `teal_data_module` creates a `shiny` module to interactively supply or modify data in a `teal` application. |
|
| 252 | +10 |
-
+ #' The module allows for running any code (creation _and_ some modification) after the app starts or reloads. |
|
| 253 | -1x | +||
| 11 | +
- get_experiment_keys <- function(mae, experiment) {
+ #' The body of the server function will be run in the app rather than in the global environment. |
||
| 254 | -5x | +||
| 12 | +
- sample_subset <- mae@sampleMap[mae@sampleMap$colname %in% colnames(experiment), ]+ #' This means it will be run every time the app starts, so use sparingly. |
||
| 255 | -5x | +||
| 13 | +
- length(unique(sample_subset$primary))+ #' |
||
| 256 | +14 |
- }+ #' Pass this module instead of a `teal_data` object in a call to [init()]. |
|
| 257 | +15 |
-
+ #' Note that the server function must always return a `teal_data` object wrapped in a reactive expression. |
|
| 258 | -1x | +||
| 16 | +
- experiment_subjects_info <- do.call("rbind", lapply(
+ #' |
||
| 259 | -1x | +||
| 17 | +
- experiment_names,+ #' See vignette `vignette("data-as-shiny-module", package = "teal")` for more details.
|
||
| 260 | -1x | +||
| 18 | +
- function(experiment_name) {
+ #' |
||
| 261 | -5x | +||
| 19 | +
- data.frame(+ #' @param ui (`function(id)`) |
||
| 262 | -5x | +||
| 20 | +
- subjects = if (!is.null(initial_data)) {
+ #' `shiny` module UI function; must only take `id` argument |
||
| 263 | -! | +||
| 21 | +
- sprintf(+ #' @param server (`function(id)`) |
||
| 264 | -! | +||
| 22 | +
- "%s/%s",+ #' `shiny` module server function; must only take `id` argument; |
||
| 265 | -! | +||
| 23 | +
- get_experiment_keys(current_data, current_data[[experiment_name]]),+ #' must return reactive expression containing `teal_data` object |
||
| 266 | -! | +||
| 24 | +
- get_experiment_keys(current_data, initial_data[[experiment_name]])+ #' @param label (`character(1)`) Label of the module. |
||
| 267 | +25 |
- )+ #' @param once (`logical(1)`) |
|
| 268 | +26 |
- } else {
+ #' If `TRUE`, the data module will be shown only once and will disappear after successful data loading. |
|
| 269 | -5x | +||
| 27 | +
- get_experiment_keys(current_data, current_data[[experiment_name]])+ #' App user will no longer be able to interact with this module anymore. |
||
| 270 | +28 |
- }+ #' If `FALSE`, the data module can be reused multiple times. |
|
| 271 | +29 |
- )+ #' App user will be able to interact and change the data output from the module multiple times. |
|
| 272 | +30 |
- }+ #' |
|
| 273 | +31 |
- ))+ #' @return |
|
| 274 | +32 |
-
+ #' `teal_data_module` returns a list of class `teal_data_module` containing two elements, `ui` and |
|
| 275 | -1x | +||
| 33 | +
- experiment_info <- cbind(experiment_obs_info, experiment_subjects_info)+ #' `server` provided via arguments. |
||
| 276 | -1x | +||
| 34 | +
- .smart_rbind(mae_info, experiment_info)+ #' |
||
| 277 | +35 |
- }+ #' @examples |
| 1 | +36 |
- #' Filter panel module in teal+ #' tdm <- teal_data_module( |
||
| 2 | +37 |
- #'+ #' ui = function(id) {
|
||
| 3 | +38 |
- #' Creates filter panel module from `teal_data` object and returns `teal_data`. It is build in a way+ #' ns <- NS(id) |
||
| 4 | +39 |
- #' that filter panel changes and anything what happens before (e.g. [`module_init_data`]) is triggering+ #' actionButton(ns("submit"), label = "Load data")
|
||
| 5 | +40 |
- #' further reactive events only if something has changed and if the module is visible. Thanks to+ #' }, |
||
| 6 | +41 |
- #' this special implementation all modules' data are recalculated only for those modules which are+ #' server = function(id) {
|
||
| 7 | +42 |
- #' currently displayed.+ #' moduleServer(id, function(input, output, session) {
|
||
| 8 | +43 |
- #'+ #' eventReactive(input$submit, {
|
||
| 9 | +44 |
- #' @return A `eventReactive` containing `teal_data` containing filtered objects and filter code.+ #' data <- within( |
||
| 10 | +45 |
- #' `eventReactive` triggers only if all conditions are met:+ #' teal_data(), |
||
| 11 | +46 |
- #' - tab is selected (`is_active`)+ #' {
|
||
| 12 | +47 |
- #' - when filters are changed (`get_filter_expr` is different than previous)+ #' dataset1 <- iris |
||
| 13 | +48 |
- #'+ #' dataset2 <- mtcars |
||
| 14 | +49 |
- #' @inheritParams module_teal_module+ #' } |
||
| 15 | +50 |
- #' @param active_datanames (`reactive` returning `character`) this module's data names+ #' ) |
||
| 16 | +51 |
- #' @name module_filter_data+ #' |
||
| 17 | +52 |
- #' @keywords internal+ #' data |
||
| 18 | +53 |
- NULL+ #' }) |
||
| 19 | +54 |
-
+ #' }) |
||
| 20 | +55 |
- #' @rdname module_filter_data+ #' } |
||
| 21 | +56 |
- ui_filter_data <- function(id) {
+ #' ) |
||
| 22 | -! | +|||
| 57 | +
- ns <- shiny::NS(id)+ #' |
|||
| 23 | -! | +|||
| 58 | +
- uiOutput(ns("panel"))
+ #' @name teal_data_module |
|||
| 24 | +59 |
- }+ #' @seealso [`teal.data::teal_data-class`], [teal.code::qenv()] |
||
| 25 | +60 |
-
+ #' |
||
| 26 | +61 |
- #' @rdname module_filter_data+ #' @export |
||
| 27 | +62 |
- srv_filter_data <- function(id, datasets, active_datanames, data_rv, is_active) {
+ teal_data_module <- function(ui, server, label = "data module", once = TRUE) {
|
||
| 28 | -86x | +63 | +33x |
- assert_reactive(datasets)+ checkmate::assert_function(ui, args = "id", nargs = 1) |
| 29 | -86x | +64 | +32x |
- moduleServer(id, function(input, output, session) {
+ checkmate::assert_function(server, args = "id", nargs = 1) |
| 30 | -86x | +65 | +30x |
- active_corrected <- reactive(intersect(active_datanames(), datasets()$datanames()))+ checkmate::assert_string(label) |
| 31 | -+ | |||
| 66 | +30x |
-
+ checkmate::assert_flag(once) |
||
| 32 | -86x | +67 | +30x |
- output$panel <- renderUI({
+ structure( |
| 33 | -88x | +68 | +30x |
- req(inherits(datasets(), "FilteredData"))+ list( |
| 34 | -88x | +69 | +30x |
- isolate({
+ ui = ui, |
| 35 | -+ | |||
| 70 | +30x |
- # render will be triggered only when FilteredData object changes (not when filters change)+ server = function(id) {
|
||
| 36 | -+ | |||
| 71 | +23x |
- # technically it means that teal_data_module needs to be refreshed+ data_out <- server(id) |
||
| 37 | -88x | +72 | +22x |
- logger::log_debug("srv_filter_panel rendering filter panel.")
+ decorate_err_msg( |
| 38 | -88x | +73 | +22x |
- if (length(active_corrected())) {
+ assert_reactive(data_out), |
| 39 | -86x | +74 | +22x |
- datasets()$srv_active("filters", active_datanames = active_corrected)
+ pre = sprintf("From: 'teal_data_module()':\nA 'teal_data_module' with \"%s\" label:", label),
|
| 40 | -86x | +75 | +22x |
- datasets()$ui_active(session$ns("filters"), active_datanames = active_corrected)
+ post = "Please make sure that this module returns a 'reactive` object containing 'teal_data' class of object." # nolint: line_length_linter. |
| 41 | +76 |
- }+ ) |
||
| 42 | +77 |
- })+ } |
||
| 43 | +78 |
- })+ ), |
||
| 44 | -+ | |||
| 79 | +30x |
-
+ label = label, |
||
| 45 | -86x | +80 | +30x |
- trigger_data <- .observe_active_filter_changed(datasets, is_active, active_corrected, data_rv)+ class = "teal_data_module", |
| 46 | -+ | |||
| 81 | +30x |
-
+ once = once |
||
| 47 | -86x | +|||
| 82 | +
- eventReactive(trigger_data(), {
+ ) |
|||
| 48 | -89x | +|||
| 83 | +
- .make_filtered_teal_data(modules, data = data_rv(), datasets = datasets(), datanames = active_corrected())+ } |
| 49 | +1 |
- })+ #' Generate lockfile for application's environment reproducibility |
||
| 50 | +2 |
- })+ #' |
||
| 51 | +3 |
- }+ #' @param lockfile_path (`character`) path to the lockfile. |
||
| 52 | +4 |
-
+ #' |
||
| 53 | +5 |
- #' @rdname module_filter_data+ #' @section Different ways of creating lockfile: |
||
| 54 | +6 |
- .make_filtered_teal_data <- function(modules, data, datasets = NULL, datanames) {
+ #' `teal` leverages [renv::snapshot()], which offers multiple methods for lockfile creation. |
||
| 55 | -89x | +|||
| 7 | +
- data <- eval_code(+ #' |
|||
| 56 | -89x | +|||
| 8 | +
- data,+ #' - **Working directory lockfile**: `teal`, by default, will create an `implicit` type lockfile that uses |
|||
| 57 | -89x | +|||
| 9 | +
- paste0(+ #' `renv::dependencies()` to detect all R packages in the current project's working directory. |
|||
| 58 | -89x | +|||
| 10 | +
- ".raw_data <- list2env(list(",
+ #' - **`DESCRIPTION`-based lockfile**: To generate a lockfile based on a `DESCRIPTION` file in your working |
|||
| 59 | -89x | +|||
| 11 | +
- toString(sprintf("%1$s = %1$s", sapply(datanames, as.name))),
+ #' directory, set `renv::settings$snapshot.type("explicit")`. The naming convention for `type` follows
|
|||
| 60 | -89x | +|||
| 12 | +
- "))\n",+ #' `renv::snapshot()`. For the `"explicit"` type, refer to `renv::settings$package.dependency.fields()` for the |
|||
| 61 | -89x | +|||
| 13 | +
- "lockEnvironment(.raw_data) # @linksto .raw_data" # this is environment and it is shared by qenvs. CAN'T MODIFY!+ #' `DESCRIPTION` fields included in the lockfile. |
|||
| 62 | +14 |
- )+ #' - **Custom files-based lockfile**: To specify custom files as the basis for the lockfile, set |
||
| 63 | +15 |
- )+ #' `renv::settings$snapshot.type("custom")` and configure the `renv.snapshot.filter` option.
|
||
| 64 | -89x | +|||
| 16 | +
- filtered_code <- .get_filter_expr(datasets = datasets, datanames = datanames)+ #' |
|||
| 65 | -89x | +|||
| 17 | +
- filtered_teal_data <- .append_evaluated_code(data, filtered_code)+ #' @section lockfile usage: |
|||
| 66 | -89x | +|||
| 18 | +
- filtered_datasets <- sapply(datanames, function(x) datasets$get_data(x, filtered = TRUE), simplify = FALSE)+ #' After creating the lockfile, you can restore the application's environment using `renv::restore()`. |
|||
| 67 | -89x | +|||
| 19 | +
- filtered_teal_data <- .append_modified_data(filtered_teal_data, filtered_datasets)+ #' |
|||
| 68 | -89x | +|||
| 20 | +
- filtered_teal_data+ #' @seealso [renv::snapshot()], [renv::restore()]. |
|||
| 69 | +21 |
- }+ #' |
||
| 70 | +22 |
-
+ #' @return `NULL` |
||
| 71 | +23 |
- #' @rdname module_filter_data+ #' |
||
| 72 | +24 |
- .observe_active_filter_changed <- function(datasets, is_active, active_datanames, data_rv) {
+ #' @name module_teal_lockfile |
||
| 73 | -86x | +|||
| 25 | +
- previous_signature <- reactiveVal(NULL)+ #' @rdname module_teal_lockfile |
|||
| 74 | -86x | +|||
| 26 | +
- filter_changed <- reactive({
+ #' |
|||
| 75 | -195x | +|||
| 27 | +
- req(inherits(datasets(), "FilteredData"))+ #' @keywords internal |
|||
| 76 | -195x | +|||
| 28 | +
- new_signature <- c(+ NULL |
|||
| 77 | -195x | +|||
| 29 | +
- teal.code::get_code(data_rv()),+ |
|||
| 78 | -195x | +|||
| 30 | +
- .get_filter_expr(datasets = datasets(), datanames = active_datanames())+ #' @rdname module_teal_lockfile |
|||
| 79 | +31 |
- )+ ui_teal_lockfile <- function(id) {
|
||
| 80 | -195x | +|||
| 32 | +! |
- if (!identical(previous_signature(), new_signature)) {
+ ns <- NS(id) |
||
| 81 | -94x | +|||
| 33 | +! |
- previous_signature(new_signature)+ shiny::tagList( |
||
| 82 | -94x | +|||
| 34 | +! |
- TRUE+ tags$span("", id = ns("lockFileStatus")),
+ |
+ ||
| 35 | +! | +
+ shinyjs::disabled(downloadLink(ns("lockFileLink"), "Download lockfile"))
|
||
| 83 | +36 |
- } else {
+ ) |
||
| 84 | -101x | +|||
| 37 | +
- FALSE+ } |
|||
| 85 | +38 |
- }+ |
||
| 86 | +39 |
- })+ #' @rdname module_teal_lockfile |
||
| 87 | +40 |
-
+ srv_teal_lockfile <- function(id) {
|
||
| 88 | -86x | +41 | +88x |
- trigger_data <- reactiveVal(NULL)+ moduleServer(id, function(input, output, session) {
|
| 89 | -86x | +42 | +88x |
- observe({
+ logger::log_debug("Initialize srv_teal_lockfile.")
|
| 90 | -208x | +43 | +88x |
- if (isTRUE(is_active() && filter_changed())) {
+ enable_lockfile_download <- function() {
|
| 91 | -94x | +|||
| 44 | +! |
- isolate({
+ shinyjs::html("lockFileStatus", "Application lockfile ready.")
|
||
| 92 | -94x | +|||
| 45 | +! |
- if (is.null(trigger_data())) {
+ shinyjs::hide("lockFileStatus", anim = TRUE)
|
||
| 93 | -86x | +|||
| 46 | +! |
- trigger_data(0)+ shinyjs::enable("lockFileLink")
+ |
+ ||
| 47 | +! | +
+ output$lockFileLink <- shiny::downloadHandler(+ |
+ ||
| 48 | +! | +
+ filename = function() {
+ |
+ ||
| 49 | +! | +
+ "renv.lock" |
||
| 94 | +50 |
- } else {
+ }, |
||
| 95 | -8x | +|||
| 51 | +! |
- trigger_data(trigger_data() + 1)+ content = function(file) {
+ |
+ ||
| 52 | +! | +
+ file.copy(lockfile_path, file) |
||
| 96 | -+ | |||
| 53 | +! |
- }+ file |
||
| 97 | +54 |
- })+ }, |
||
| 98 | -+ | |||
| 55 | +! |
- }+ contentType = "application/json" |
||
| 99 | +56 |
- })+ ) |
||
| 100 | +57 |
-
+ } |
||
| 101 | -86x | +58 | +88x |
- trigger_data+ disable_lockfile_download <- function() {
|
| 102 | -+ | |||
| 59 | +! |
- }+ warning("Lockfile creation failed.", call. = FALSE)
|
||
| 103 | -+ | |||
| 60 | +! |
-
+ shinyjs::html("lockFileStatus", "Lockfile creation failed.")
+ |
+ ||
| 61 | +! | +
+ shinyjs::hide("lockFileLink")
|
||
| 104 | +62 |
- #' @rdname module_filter_data+ } |
||
| 105 | +63 |
- .get_filter_expr <- function(datasets, datanames) {
+
|
||
| 106 | -284x | +64 | +88x |
- if (length(datanames)) {
+ shiny::onStop(function() {
|
| 107 | -278x | +65 | +88x |
- teal.slice::get_filter_expr(datasets = datasets, datanames = datanames)+ if (file.exists(lockfile_path) && !shiny::isRunning()) {
|
| 108 | -+ | |||
| 66 | +1x |
- } else {
+ logger::log_debug("Removing lockfile after shutting down the app")
|
||
| 109 | -6x | +67 | +1x |
- NULL+ file.remove(lockfile_path) |
| 110 | +68 |
- }+ } |
||
| 111 | +69 |
- }+ }) |
| 1 | +70 |
- #' `teal_data` utils+ |
||
| 2 | -+ | |||
| 71 | +88x |
- #'+ lockfile_path <- "teal_app.lock" |
||
| 3 | -+ | |||
| 72 | +88x |
- #' In `teal` we need to recreate the `teal_data` object due to two operations:+ mode <- getOption("teal.lockfile.mode", default = "")
|
||
| 4 | +73 |
- #' - we need to append filter-data code and objects which have been evaluated in `FilteredData` and+ |
||
| 5 | -+ | |||
| 74 | +88x |
- #' we want to avoid double-evaluation.+ if (!(mode %in% c("auto", "enabled", "disabled"))) {
|
||
| 6 | -+ | |||
| 75 | +! |
- #' - we need to subset `teal_data` to `datanames` used by the module, to shorten obtainable R-code+ stop("'teal.lockfile.mode' option can only be one of \"auto\", \"disabled\" or \"disabled\". ")
|
||
| 7 | +76 |
- #'+ } |
||
| 8 | +77 |
- #' Due to above recreation of `teal_data` object can't be done simply by using public+ |
||
| 9 | -+ | |||
| 78 | +88x |
- #' `teal.code` and `teal.data` methods.+ if (mode == "disabled") {
|
||
| 10 | -+ | |||
| 79 | +1x |
- #'+ logger::log_debug("'teal.lockfile.mode' option is set to 'disabled'. Hiding lockfile download button.")
|
||
| 11 | -+ | |||
| 80 | +1x |
- #' @param data (`teal_data`)+ shinyjs::hide("lockFileLink")
|
||
| 12 | -+ | |||
| 81 | +1x |
- #' @param code (`character`) code to append to the object's code slot.+ return(NULL) |
||
| 13 | +82 |
- #' @param objects (`list`) objects to append to object's environment.+ } |
||
| 14 | +83 |
- #' @return modified `teal_data`+ |
||
| 15 | -+ | |||
| 84 | +87x |
- #' @keywords internal+ if (file.exists(lockfile_path)) {
|
||
| 16 | -+ | |||
| 85 | +! |
- #' @name teal_data_utilities+ logger::log_debug("Lockfile has already been created for this app - skipping automatic creation.")
|
||
| 17 | -+ | |||
| 86 | +! |
- NULL+ enable_lockfile_download() |
||
| 18 | -+ | |||
| 87 | +! |
-
+ return(NULL) |
||
| 19 | +88 |
- #' @rdname teal_data_utilities+ } |
||
| 20 | +89 |
- .append_evaluated_code <- function(data, code) {
- |
- ||
| 21 | -89x | -
- checkmate::assert_class(data, "teal_data")+ |
||
| 22 | -89x | +90 | +87x |
- data@code <- c(data@code, code2list(code))+ if (mode == "auto" && .is_disabled_lockfile_scenario()) {
|
| 23 | -89x | +91 | +86x |
- methods::validObject(data)+ logger::log_debug( |
| 24 | -89x | +92 | +86x |
- data+ "Automatic lockfile creation disabled. Execution scenario satisfies teal:::.is_disabled_lockfile_scenario()." |
| 25 | +93 |
- }+ ) |
||
| 26 | -+ | |||
| 94 | +86x |
-
+ shinyjs::hide("lockFileLink")
|
||
| 27 | -+ | |||
| 95 | +86x |
- #' @rdname teal_data_utilities+ return(NULL) |
||
| 28 | +96 |
- .append_modified_data <- function(data, objects) {
+ } |
||
| 29 | -89x | +|||
| 97 | +
- checkmate::assert_class(data, "teal_data")+ |
|||
| 30 | -89x | +98 | +1x |
- checkmate::assert_class(objects, "list")+ if (!.is_lockfile_deps_installed()) {
|
| 31 | -89x | +|||
| 99 | +! |
- new_env <- list2env(objects, parent = .GlobalEnv)+ warning("Automatic lockfile creation disabled. `mirai` and `renv` packages must be installed.")
|
||
| 32 | -89x | +|||
| 100 | +! |
- rlang::env_coalesce(new_env, as.environment(data))+ shinyjs::hide("lockFileLink")
|
||
| 33 | -89x | +|||
| 101 | +! |
- data@.xData <- new_env+ return(NULL) |
||
| 34 | -89x | +|||
| 102 | +
- data+ } |
|||
| 35 | +103 |
- }+ |
| 1 | +104 |
- #' UI and server modules of `teal`+ # - Will be run only if the lockfile doesn't exist (see the if-s above) |
|
| 2 | +105 |
- #'+ # - We render to the tempfile because the process might last after session is closed and we don't |
|
| 3 | +106 |
- #' @description `r lifecycle::badge("deprecated")`
+ # want to make a "teal_app.renv" then. This is why we copy only during active session. |
|
| 4 | -+ | ||
| 107 | +1x |
- #' Please use [`module_teal`] instead.+ process <- .teal_lockfile_process_invoke(lockfile_path) |
|
| 5 | -+ | ||
| 108 | +1x |
- #'+ observeEvent(process$status(), {
|
|
| 6 | -+ | ||
| 109 | +! |
- #' @inheritParams ui_teal+ if (process$status() %in% c("initial", "running")) {
|
|
| 7 | -+ | ||
| 110 | +! |
- #' @inheritParams srv_teal+ shinyjs::html("lockFileStatus", "Creating lockfile...")
|
|
| 8 | -+ | ||
| 111 | +! |
- #'+ } else if (process$status() == "success") {
|
|
| 9 | -+ | ||
| 112 | +! |
- #' @return+ result <- process$result() |
|
| 10 | -+ | ||
| 113 | +! |
- #' Returns a `reactive` expression containing a `teal_data` object when data is loaded or `NULL` when it is not.+ if (any(grepl("Lockfile written to", result$out))) {
|
|
| 11 | -+ | ||
| 114 | +! |
- #' @name module_teal_with_splash+ logger::log_debug("Lockfile containing { length(result$res$Packages) } packages created.")
|
|
| 12 | -+ | ||
| 115 | +! |
- #'+ if (any(grepl("(WARNING|ERROR):", result$out))) {
|
|
| 13 | -+ | ||
| 116 | +! |
- NULL+ warning("Lockfile created with warning(s) or error(s):", call. = FALSE)
|
|
| 14 | -+ | ||
| 117 | +! |
-
+ for (i in result$out) {
|
|
| 15 | -+ | ||
| 118 | +! |
- #' @export+ warning(i, call. = FALSE) |
|
| 16 | +119 |
- #' @rdname module_teal_with_splash+ } |
|
| 17 | +120 |
- ui_teal_with_splash <- function(id,+ } |
|
| 18 | -+ | ||
| 121 | +! |
- data,+ enable_lockfile_download() |
|
| 19 | +122 |
- title = build_app_title(),+ } else {
|
|
| 20 | -+ | ||
| 123 | +! |
- header = tags$p(),+ disable_lockfile_download() |
|
| 21 | +124 |
- footer = tags$p()) {
+ } |
|
| 22 | +125 | ! |
- lifecycle::deprecate_soft(+ } else if (process$status() == "error") {
|
| 23 | +126 | ! |
- when = "0.16",+ disable_lockfile_download() |
| 24 | -! | +||
| 127 | +
- what = "ui_teal_with_splash()",+ } |
||
| 25 | -! | +||
| 128 | ++ |
+ })+ |
+ |
| 129 | ++ | + + | +|
| 130 | +1x |
- details = "Deprecated, please use `ui_teal` instead"+ NULL |
|
| 26 | +131 |
- )+ }) |
|
| 27 | -! | +||
| 132 | +
- ui_teal(id = id, title = title, header = header, footer = footer)+ } |
||
| 28 | +133 |
- }+ |
|
| 29 | +134 |
-
+ utils::globalVariables(c("opts", "sysenv", "libpaths", "wd", "lockfilepath", "run")) # needed for mirai call
|
|
| 30 | +135 |
- #' @export+ #' @rdname module_teal_lockfile |
|
| 31 | +136 |
- #' @rdname module_teal_with_splash+ .teal_lockfile_process_invoke <- function(lockfile_path) {
+ |
+ |
| 137 | +1x | +
+ mirai_obj <- NULL+ |
+ |
| 138 | +1x | +
+ process <- shiny::ExtendedTask$new(function() {
+ |
+ |
| 139 | +1x | +
+ m <- mirai::mirai( |
|
| 32 | +140 |
- srv_teal_with_splash <- function(id, data, modules, filter = teal_slices()) {
+ {
|
|
| 33 | -! | +||
| 141 | +1x |
- lifecycle::deprecate_soft(+ options(opts) |
|
| 34 | -! | +||
| 142 | +1x |
- when = "0.16",+ do.call(Sys.setenv, sysenv) |
|
| 35 | -! | +||
| 143 | +1x |
- what = "srv_teal_with_splash()",+ .libPaths(libpaths) |
|
| 36 | -! | +||
| 144 | +1x |
- details = "Deprecated, please use `srv_teal` instead"+ setwd(wd)+ |
+ |
| 145 | +1x | +
+ run(lockfile_path = lockfile_path) |
|
| 37 | +146 |
- )+ }, |
|
| 38 | -! | +||
| 147 | +1x |
- srv_teal(id = id, data = data, modules = modules, filter = filter)+ run = .renv_snapshot, |
|
| 39 | -+ | ||
| 148 | +1x |
- }+ lockfile_path = lockfile_path, |
| 1 | -+ | ||
| 149 | +1x |
- #' Data module for `teal` transformations and output customization+ opts = options(), |
|
| 2 | -+ | ||
| 150 | +1x |
- #'+ libpaths = .libPaths(), |
|
| 3 | -+ | ||
| 151 | +1x |
- #' @description+ sysenv = as.list(Sys.getenv()), |
|
| 4 | -+ | ||
| 152 | +1x |
- #' `r lifecycle::badge("experimental")`
+ wd = getwd() |
|
| 5 | +153 |
- #'+ ) |
|
| 6 | -+ | ||
| 154 | +1x |
- #' `teal_transform_module` provides a `shiny` module that enables data transformations within a `teal` application+ mirai_obj <<- m |
|
| 7 | -+ | ||
| 155 | +1x |
- #' and allows for customization of outputs generated by modules.+ m |
|
| 8 | +156 |
- #'+ }) |
|
| 9 | +157 |
- #' # Transforming Module Inputs in `teal`+ |
|
| 10 | -+ | ||
| 158 | +1x |
- #'+ shiny::onStop(function() {
|
|
| 11 | -+ | ||
| 159 | +1x |
- #' Data transformations occur after data has been filtered in `teal`.+ if (mirai::unresolved(mirai_obj)) {
|
|
| 12 | -+ | ||
| 160 | +! |
- #' The transformed data is then passed to the `server` of [`teal_module()`] and managed by `teal`'s internal processes.+ logger::log_debug("Terminating a running lockfile process...")
|
|
| 13 | -+ | ||
| 161 | +! |
- #' The primary advantage of `teal_transform_module` over custom modules is in its error handling, where all warnings and+ mirai::stop_mirai(mirai_obj) # this doesn't stop running - renv will be created even if session is closed |
|
| 14 | +162 |
- #' errors are managed by `teal`, allowing developers to focus on transformation logic.+ } |
|
| 15 | +163 |
- #'+ }) |
|
| 16 | +164 |
- #' For more details, see the vignette: `vignette("data-transform-as-shiny-module", package = "teal")`.
+
|
|
| 17 | -+ | ||
| 165 | +1x |
- #'+ suppressWarnings({ # 'package:stats' may not be available when loading
|
|
| 18 | -+ | ||
| 166 | +1x |
- #' # Customizing Module Outputs+ process$invoke() |
|
| 19 | +167 |
- #'+ }) |
|
| 20 | +168 |
- #' `teal_transform_module` also allows developers to modify any object created within [`teal.data::teal_data`].+ |
|
| 21 | -+ | ||
| 169 | +1x |
- #' This means you can use it to customize not only datasets but also tables, listings, and graphs.+ logger::log_debug("Lockfile creation started based on { getwd() }.")
|
|
| 22 | +170 |
- #' Some [`teal_modules`] permit developers to inject custom `shiny` modules to enhance displayed outputs.+ |
|
| 23 | -+ | ||
| 171 | +1x |
- #' To manage these `decorators` within your module, use [`ui_transform_teal_data()`] and [`srv_transform_teal_data()`].+ process |
|
| 24 | +172 |
- #' (For further guidance on managing decorators, refer to `ui_args` and `srv_args` in the vignette documentation.)+ } |
|
| 25 | +173 |
- #'+ |
|
| 26 | +174 |
- #' See the vignette `vignette("decorate-modules-output", package = "teal")` for additional examples.
+ #' @rdname module_teal_lockfile |
|
| 27 | +175 |
- #'+ .renv_snapshot <- function(lockfile_path) {
|
|
| 28 | -+ | ||
| 176 | +1x |
- #' # `server` as a language+ out <- utils::capture.output( |
|
| 29 | -+ | ||
| 177 | +1x |
- #'+ res <- renv::snapshot( |
|
| 30 | -+ | ||
| 178 | +1x |
- #' The `server` function in `teal_transform_module` must return a reactive [`teal.data::teal_data`] object.+ lockfile = lockfile_path, |
|
| 31 | -+ | ||
| 179 | +1x |
- #' For simple transformations without complex reactivity, the `server` function might look like this:s+ prompt = FALSE, |
|
| 32 | -+ | ||
| 180 | +1x |
- #'+ force = TRUE, |
|
| 33 | -+ | ||
| 181 | +1x |
- #' ```+ type = renv::settings$snapshot.type() # see the section "Different ways of creating lockfile" above here |
|
| 34 | +182 |
- #' function(id, data) {
+ ) |
|
| 35 | +183 |
- #' moduleServer(id, function(input, output, session) {
+ ) |
|
| 36 | +184 |
- #' reactive({
+
|
|
| 37 | -+ | ||
| 185 | +1x |
- #' within(+ list(out = out, res = res) |
|
| 38 | +186 |
- #' data(),+ } |
|
| 39 | +187 |
- #' expr = x <- subset(x, col == level),+ |
|
| 40 | +188 |
- #' level = input$level+ #' @rdname module_teal_lockfile |
|
| 41 | +189 |
- #' )+ .is_lockfile_deps_installed <- function() {
|
|
| 42 | -+ | ||
| 190 | +1x |
- #' })+ requireNamespace("mirai", quietly = TRUE) && requireNamespace("renv", quietly = TRUE)
|
|
| 43 | +191 |
- #' })+ } |
|
| 44 | +192 |
- #' }+ |
|
| 45 | +193 |
- #' ```+ #' @rdname module_teal_lockfile |
|
| 46 | +194 |
- #'+ .is_disabled_lockfile_scenario <- function() {
|
|
| 47 | -+ | ||
| 195 | +86x |
- #' The example above can be simplified using `make_teal_transform_server`, where `level` is automatically matched to the+ identical(Sys.getenv("CALLR_IS_RUNNING"), "true") || # inside callr process
|
|
| 48 | -+ | ||
| 196 | +86x |
- #' corresponding `input` parameter:+ identical(Sys.getenv("TESTTHAT"), "true") || # inside devtools::test
|
|
| 49 | -+ | ||
| 197 | +86x |
- #'+ !identical(Sys.getenv("QUARTO_PROJECT_ROOT"), "") || # inside Quarto process
|
|
| 50 | +198 |
- #' ```+ ( |
|
| 51 | -+ | ||
| 199 | +86x |
- #' make_teal_transform_server(expr = expression(x <- subset(x, col == level)))+ ("CheckExEnv" %in% search()) || any(c("_R_CHECK_TIMINGS_", "_R_CHECK_LICENSE_") %in% names(Sys.getenv()))
|
|
| 52 | -+ | ||
| 200 | +86x |
- #' ```+ ) # inside R CMD CHECK |
|
| 53 | +201 |
- #' @inheritParams teal_data_module+ } |
| 54 | +1 |
- #' @param server (`function(id, data)` or `expression`)+ #' Module to transform `reactive` `teal_data` |
||
| 55 | +2 |
- #' A `shiny` module server function that takes `id` and `data` as arguments, where `id` is the module id and `data`+ #' |
||
| 56 | +3 |
- #' is the reactive `teal_data` input. The `server` function must return a reactive expression containing a `teal_data`+ #' Module calls [teal_transform_module()] in sequence so that `reactive teal_data` output |
||
| 57 | +4 |
- #' object. For simplified syntax, use [`make_teal_transform_server()`].+ #' from one module is handed over to the following module's input. |
||
| 58 | +5 |
- #' @param datanames (`character`)+ #' |
||
| 59 | +6 |
- #' Specifies the names of datasets relevant to the module. Only filters for the specified `datanames` will be displayed+ #' @inheritParams module_teal_data |
||
| 60 | +7 |
- #' in the filter panel. The keyword `"all"` can be used to display filters for all datasets. `datanames` are+ #' @inheritParams teal_modules |
||
| 61 | +8 |
- #' automatically appended to the [`modules()`] `datanames`.+ #' @param class (character(1)) CSS class to be added in the `div` wrapper tag. |
||
| 62 | +9 |
- #'+ |
||
| 63 | +10 |
- #'+ #' @return `reactive` `teal_data` |
||
| 64 | +11 |
- #' @examples+ #' |
||
| 65 | +12 |
- #' data_transformators <- list(+ #' @name module_transform_data |
||
| 66 | +13 |
- #' teal_transform_module(+ NULL |
||
| 67 | +14 |
- #' label = "Static transformator for iris",+ |
||
| 68 | +15 |
- #' datanames = "iris",+ #' @export |
||
| 69 | +16 |
- #' server = function(id, data) {
+ #' @rdname module_transform_data |
||
| 70 | +17 |
- #' moduleServer(id, function(input, output, session) {
+ ui_transform_teal_data <- function(id, transformators, class = "well") {
|
||
| 71 | -+ | |||
| 18 | +1x |
- #' reactive({
+ checkmate::assert_string(id) |
||
| 72 | -+ | |||
| 19 | +1x |
- #' within(data(), {
+ if (length(transformators) == 0L) {
|
||
| 73 | -+ | |||
| 20 | +! |
- #' iris <- head(iris, 5)+ return(NULL) |
||
| 74 | +21 |
- #' })+ } |
||
| 75 | -+ | |||
| 22 | +1x |
- #' })+ if (inherits(transformators, "teal_transform_module")) {
|
||
| 76 | -+ | |||
| 23 | +1x |
- #' })+ transformators <- list(transformators) |
||
| 77 | +24 |
- #' }+ } |
||
| 78 | -+ | |||
| 25 | +1x |
- #' ),+ checkmate::assert_list(transformators, "teal_transform_module") |
||
| 79 | -+ | |||
| 26 | +1x |
- #' teal_transform_module(+ names(transformators) <- sprintf("transform_%d", seq_len(length(transformators)))
|
||
| 80 | +27 |
- #' label = "Interactive transformator for iris",+ |
||
| 81 | -+ | |||
| 28 | +1x |
- #' datanames = "iris",+ lapply( |
||
| 82 | -+ | |||
| 29 | +1x |
- #' ui = function(id) {
+ names(transformators), |
||
| 83 | -+ | |||
| 30 | +1x |
- #' ns <- NS(id)+ function(name) {
|
||
| 84 | -+ | |||
| 31 | +1x |
- #' tags$div(+ child_id <- NS(id, name) |
||
| 85 | -+ | |||
| 32 | +1x |
- #' numericInput(ns("n_cols"), "Show n columns", value = 5, min = 1, max = 5, step = 1)
+ ns <- NS(child_id) |
||
| 86 | -+ | |||
| 33 | +1x |
- #' )+ data_mod <- transformators[[name]] |
||
| 87 | -+ | |||
| 34 | +1x |
- #' },+ transform_wrapper_id <- ns(sprintf("wrapper_%s", name))
|
||
| 88 | +35 |
- #' server = function(id, data) {
+
|
||
| 89 | -+ | |||
| 36 | +1x |
- #' moduleServer(id, function(input, output, session) {
+ display_fun <- if (is.null(data_mod$ui)) shinyjs::hidden else function(x) x |
||
| 90 | +37 |
- #' reactive({
+
|
||
| 91 | -+ | |||
| 38 | +1x |
- #' within(data(),+ display_fun( |
||
| 92 | -+ | |||
| 39 | +1x |
- #' {
+ div( |
||
| 93 | +40 |
- #' iris <- iris[, 1:n_cols]+ # class .teal_validated changes the color of the boarder on error in ui_validate_reactive_teal_data |
||
| 94 | +41 |
- #' },+ # For details see tealValidate.js file. |
||
| 95 | -+ | |||
| 42 | +1x |
- #' n_cols = input$n_cols+ id = ns("wrapper"),
|
||
| 96 | -+ | |||
| 43 | +1x |
- #' )+ class = c(class, "teal_validated"), |
||
| 97 | -+ | |||
| 44 | +1x |
- #' })+ title = attr(data_mod, "label"), |
||
| 98 | -+ | |||
| 45 | +1x |
- #' })+ tags$span( |
||
| 99 | -+ | |||
| 46 | +1x |
- #' }+ class = "text-primary mb-4", |
||
| 100 | -+ | |||
| 47 | +1x |
- #' )+ icon("fas fa-square-pen"),
|
||
| 101 | -+ | |||
| 48 | +1x |
- #' )+ attr(data_mod, "label") |
||
| 102 | +49 |
- #'+ ), |
||
| 103 | -+ | |||
| 50 | +1x |
- #' output_decorator <- teal_transform_module(+ tags$i( |
||
| 104 | -+ | |||
| 51 | +1x |
- #' server = make_teal_transform_server(+ class = "remove pull-right fa fa-angle-down", |
||
| 105 | -+ | |||
| 52 | +1x |
- #' expression(+ style = "cursor: pointer;", |
||
| 106 | -+ | |||
| 53 | +1x |
- #' object <- rev(object)+ title = "fold/expand transformator panel", |
||
| 107 | -+ | |||
| 54 | +1x |
- #' )+ onclick = sprintf("togglePanelItems(this, '%s', 'fa-angle-right', 'fa-angle-down');", transform_wrapper_id)
|
||
| 108 | +55 |
- #' )+ ), |
||
| 109 | -+ | |||
| 56 | +1x |
- #' )+ tags$div( |
||
| 110 | -+ | |||
| 57 | +1x |
- #'+ id = transform_wrapper_id, |
||
| 111 | -+ | |||
| 58 | +1x |
- #' app <- init(+ if (is.null(data_mod$ui)) {
|
||
| 112 | -+ | |||
| 59 | +! |
- #' data = teal_data(iris = iris),+ return(NULL) |
||
| 113 | +60 |
- #' modules = example_module(+ } else {
|
||
| 114 | -+ | |||
| 61 | +1x |
- #' transformators = data_transformators,+ data_mod$ui(id = ns("transform"))
|
||
| 115 | +62 |
- #' decorators = list(output_decorator)+ }, |
||
| 116 | -+ | |||
| 63 | +1x |
- #' )+ div( |
||
| 117 | -+ | |||
| 64 | +1x |
- #' )+ id = ns("validate_messages"),
|
||
| 118 | -+ | |||
| 65 | +1x |
- #' if (interactive()) {
+ class = "teal_validated", |
||
| 119 | -+ | |||
| 66 | +1x |
- #' shinyApp(app$ui, app$server)+ uiOutput(ns("error_wrapper"))
|
||
| 120 | +67 |
- #' }+ ) |
||
| 121 | +68 |
- #'+ ) |
||
| 122 | +69 |
- #' @name teal_transform_module+ ) |
||
| 123 | +70 |
- #'+ ) |
||
| 124 | +71 |
- #' @export+ } |
||
| 125 | +72 |
- teal_transform_module <- function(ui = NULL,+ ) |
||
| 126 | +73 |
- server = function(id, data) data,+ } |
||
| 127 | +74 |
- label = "transform module",+ |
||
| 128 | +75 |
- datanames = "all") {
+ #' @export |
||
| 129 | -25x | +|||
| 76 | +
- structure(+ #' @rdname module_transform_data |
|||
| 130 | -25x | +|||
| 77 | +
- list(+ srv_transform_teal_data <- function(id, data, transformators, modules = NULL, is_transform_failed = reactiveValues()) {
|
|||
| 131 | -25x | +78 | +94x |
- ui = ui,+ checkmate::assert_string(id) |
| 132 | -25x | +79 | +94x |
- server = function(id, data) {
+ assert_reactive(data) |
| 133 | -26x | +80 | +94x |
- data_out <- server(id, data)+ checkmate::assert_class(modules, "teal_module", null.ok = TRUE) |
| 134 | -+ | |||
| 81 | +94x |
-
+ if (length(transformators) == 0L) {
|
||
| 135 | -26x | +82 | +71x |
- if (inherits(data_out, "reactive.event")) {
+ return(data) |
| 136 | +83 |
- # This warning message partially detects when `eventReactive` is used in `data_module`.- |
- ||
| 137 | -1x | -
- warning(+ } |
||
| 138 | -1x | +84 | +23x |
- "teal_transform_module() ",+ if (inherits(transformators, "teal_transform_module")) {
|
| 139 | -1x | +85 | +3x |
- "Using eventReactive in teal_transform module server code should be avoided as it ",+ transformators <- list(transformators) |
| 140 | -1x | +|||
| 86 | +
- "may lead to unexpected behavior. See the vignettes for more information ",+ } |
|||
| 141 | -1x | +87 | +23x |
- "(`vignette(\"data-transform-as-shiny-module\", package = \"teal\")`).",+ checkmate::assert_list(transformators, "teal_transform_module", null.ok = TRUE) |
| 142 | -1x | +88 | +23x |
- call. = FALSE+ names(transformators) <- sprintf("transform_%d", seq_len(length(transformators)))
|
| 143 | +89 |
- )+ |
||
| 144 | -+ | |||
| 90 | +23x |
- }+ moduleServer(id, function(input, output, session) {
|
||
| 145 | -+ | |||
| 91 | +23x |
-
+ module_output <- Reduce( |
||
| 146 | -+ | |||
| 92 | +23x |
-
+ function(data_previous, name) {
|
||
| 147 | +93 | 26x |
- decorate_err_msg(+ moduleServer(name, function(input, output, session) {
|
|
| 148 | +94 | 26x |
- assert_reactive(data_out),+ logger::log_debug("srv_transform_teal_data initializing for { name }.")
|
|
| 149 | +95 | 26x |
- pre = sprintf("From: 'teal_transform_module()':\nA 'teal_transform_module' with \"%s\" label:", label),
+ is_transform_failed[[name]] <- FALSE |
|
| 150 | +96 | 26x |
- post = "Please make sure that this module returns a 'reactive` object containing 'teal_data' class of object." # nolint: line_length_linter.+ data_out <- transformators[[name]]$server("transform", data = data_previous)
|
|
| 151 | -+ | |||
| 97 | +26x |
- )+ data_handled <- reactive(tryCatch(data_out(), error = function(e) e)) |
||
| 152 | -+ | |||
| 98 | +26x |
- }+ observeEvent(data_handled(), {
|
||
| 153 | -+ | |||
| 99 | +32x |
- ),+ if (inherits(data_handled(), "teal_data")) {
|
||
| 154 | -25x | +100 | +22x |
- label = label,+ is_transform_failed[[name]] <- FALSE |
| 155 | -25x | +|||
| 101 | +
- datanames = datanames,+ } else {
|
|||
| 156 | -25x | +102 | +10x |
- class = c("teal_transform_module", "teal_data_module")
+ is_transform_failed[[name]] <- TRUE |
| 157 | +103 |
- )+ } |
||
| 158 | +104 |
- }+ }) |
||
| 159 | +105 | |||
| 160 | -+ | |||
| 106 | +26x |
- #' Make teal_transform_module's server+ is_previous_failed <- reactive({
|
||
| 161 | -+ | |||
| 107 | +29x |
- #'+ idx_this <- which(names(is_transform_failed) == name) |
||
| 162 | -+ | |||
| 108 | +29x |
- #' A factory function to simplify creation of a [`teal_transform_module`]'s server. Specified `expr`+ is_transform_failed_list <- reactiveValuesToList(is_transform_failed) |
||
| 163 | -+ | |||
| 109 | +29x |
- #' is wrapped in a shiny module function and output can be passed to the `server` argument in+ idx_failures <- which(unlist(is_transform_failed_list)) |
||
| 164 | -+ | |||
| 110 | +29x |
- #' [teal_transform_module()] call. Such a server function can be linked with ui and values from the+ any(idx_failures < idx_this) |
||
| 165 | +111 |
- #' inputs can be used in the expression. Object names specified in the expression will be substituted+ }) |
||
| 166 | +112 |
- #' with the value of the respective input (matched by the name) - for example in+ |
||
| 167 | -+ | |||
| 113 | +26x |
- #' `expression(graph <- graph + ggtitle(title))` object `title` will be replaced with the value of+ srv_validate_error("silent_error", data_handled, validate_shiny_silent_error = FALSE)
|
||
| 168 | -+ | |||
| 114 | +26x |
- #' `input$title`.+ srv_check_class_teal_data("class_teal_data", data_handled)
|
||
| 169 | -+ | |||
| 115 | +26x |
- #' @param expr (`language`)+ if (!is.null(modules)) {
|
||
| 170 | -+ | |||
| 116 | +20x |
- #' An R call which will be evaluated within [`teal.data::teal_data`] environment.+ srv_check_module_datanames("datanames_warning", data_handled, modules)
|
||
| 171 | +117 |
- #' @return `function(id, data)` returning `shiny` module+ } |
||
| 172 | +118 |
- #' @examples+ |
||
| 173 | +119 |
- #'+ # When there is no UI (`ui = NULL`) it should still show the errors |
||
| 174 | -+ | |||
| 120 | +26x |
- #' trim_iris <- teal_transform_module(+ observe({
|
||
| 175 | -+ | |||
| 121 | +32x |
- #' label = "Simplified interactive transformator for iris",+ if (!inherits(data_handled(), "teal_data") && !is_previous_failed()) {
|
||
| 176 | -+ | |||
| 122 | +10x |
- #' datanames = "iris",+ shinyjs::show("wrapper")
|
||
| 177 | +123 |
- #' ui = function(id) {
+ } |
||
| 178 | +124 |
- #' ns <- NS(id)+ }) |
||
| 179 | +125 |
- #' numericInput(ns("n_rows"), "Subset n rows", value = 6, min = 1, max = 150, step = 1)
+
|
||
| 180 | -+ | |||
| 126 | +26x |
- #' },+ transform_wrapper_id <- sprintf("wrapper_%s", name)
|
||
| 181 | -+ | |||
| 127 | +26x |
- #' server = make_teal_transform_server(expression(iris <- head(iris, n_rows)))+ output$error_wrapper <- renderUI({
|
||
| 182 | -+ | |||
| 128 | +29x |
- #' )+ if (is_previous_failed()) {
|
||
| 183 | -+ | |||
| 129 | +! |
- #'+ shinyjs::disable(transform_wrapper_id) |
||
| 184 | -+ | |||
| 130 | +! |
- #' app <- init(+ tags$div("One of previous transformators failed. Please check its inputs.", class = "teal-output-warning")
|
||
| 185 | +131 |
- #' data = teal_data(iris = iris),+ } else {
|
||
| 186 | -+ | |||
| 132 | +29x |
- #' modules = example_module(transformators = trim_iris)+ shinyjs::enable(transform_wrapper_id) |
||
| 187 | -+ | |||
| 133 | +29x |
- #' )+ shiny::tagList( |
||
| 188 | -+ | |||
| 134 | +29x |
- #' if (interactive()) {
+ ui_validate_error(session$ns("silent_error")),
|
||
| 189 | -+ | |||
| 135 | +29x |
- #' shinyApp(app$ui, app$server)+ ui_check_class_teal_data(session$ns("class_teal_data")),
|
||
| 190 | -+ | |||
| 136 | +29x |
- #' }+ ui_check_module_datanames(session$ns("datanames_warning"))
|
||
| 191 | +137 |
- #'+ ) |
||
| 192 | +138 |
- #' @export+ } |
||
| 193 | +139 |
- make_teal_transform_server <- function(expr) {
+ }) |
||
| 194 | -3x | +|||
| 140 | +
- if (is.call(expr)) {
+
|
|||
| 195 | -1x | +141 | +26x |
- expr <- as.expression(expr)+ .trigger_on_success(data_handled) |
| 196 | +142 |
- }- |
- ||
| 197 | -3x | -
- checkmate::assert_multi_class(expr, c("call", "expression"))
+ }) |
||
| 198 | +143 |
-
+ }, |
||
| 199 | -3x | +144 | +23x |
- function(id, data) {
+ x = names(transformators), |
| 200 | -3x | +145 | +23x |
- moduleServer(id, function(input, output, session) {
+ init = data |
| 201 | -3x | +|||
| 146 | +
- list_env <- reactive(+ ) |
|||
| 202 | -3x | +147 | +23x |
- lapply(rlang::set_names(names(input)), function(x) input[[x]])+ module_output |
| 203 | +148 |
- )+ }) |
||
| 204 | +149 |
-
+ } |
||
| 205 | -3x | +
| 1 | +
- reactive({
+ #' Create a `tdata` object |
||
| 206 | -4x | +||
| 2 | +
- call_with_inputs <- lapply(expr, function(x) {
+ #' |
||
| 207 | -4x | +||
| 3 | +
- do.call(what = substitute, args = list(expr = x, env = list_env()))+ #' @description `r lifecycle::badge("superseded")`
|
||
| 208 | +4 |
- })+ #' |
|
| 209 | -4x | +||
| 5 | +
- eval_code(object = data(), code = as.expression(call_with_inputs))+ #' Recent changes in `teal` cause modules to fail because modules expect a `tdata` object |
||
| 210 | +6 |
- })+ #' to be passed to the `data` argument but instead they receive a `teal_data` object, |
|
| 211 | +7 |
- })+ #' which is additionally wrapped in a reactive expression in the server functions. |
|
| 212 | +8 |
- }+ #' In order to easily adapt such modules without a proper refactor, |
|
| 213 | +9 |
- }+ #' use this function to downgrade the `data` argument. |
|
| 214 | +10 |
-
+ #' |
|
| 215 | +11 |
- #' Extract all `transformators` from `modules`.+ #' @name tdata |
|
| 216 | +12 |
- #'+ #' @param ... ignored |
|
| 217 | +13 |
- #' @param modules `teal_modules` or `teal_module`+ #' @return nothing |
|
| 218 | +14 |
- #' @return A list of `teal_transform_module` nested in the same way as input `modules`.+ NULL |
|
| 219 | +15 |
- #' @keywords internal+ |
|
| 220 | +16 |
- extract_transformators <- function(modules) {
+ #' @rdname tdata |
|
| 221 | -10x | +||
| 17 | +
- if (inherits(modules, "teal_module")) {
+ #' @export |
||
| 222 | -5x | +||
| 18 | +
- modules$transformators+ new_tdata <- function(...) {
|
||
| 223 | -5x | +||
| 19 | +! |
- } else if (inherits(modules, "teal_modules")) {
+ .deprecate_tdata_msg() |
|
| 224 | -5x | +||
| 20 | +
- lapply(modules$children, extract_transformators)+ } |
||
| 225 | +21 |
- }+ |
|
| 226 | +22 |
- }+ #' @rdname tdata |
| 1 | +23 |
- #' Data module for `teal` applications+ #' @export |
|
| 2 | +24 |
- #'+ tdata2env <- function(...) {
|
|
| 3 | -+ | ||
| 25 | +! |
- #' @description+ .deprecate_tdata_msg() |
|
| 4 | +26 |
- #' `r lifecycle::badge("experimental")`
+ } |
|
| 5 | +27 |
- #'+ |
|
| 6 | +28 |
- #' Create a `teal_data_module` object and evaluate code on it with history tracking.+ #' @rdname tdata |
|
| 7 | +29 |
- #'+ #' @export |
|
| 8 | +30 |
- #' @details+ get_code_tdata <- function(...) {
|
|
| 9 | -+ | ||
| 31 | +! |
- #' `teal_data_module` creates a `shiny` module to interactively supply or modify data in a `teal` application.+ .deprecate_tdata_msg() |
|
| 10 | +32 |
- #' The module allows for running any code (creation _and_ some modification) after the app starts or reloads.+ } |
|
| 11 | +33 |
- #' The body of the server function will be run in the app rather than in the global environment.+ |
|
| 12 | +34 |
- #' This means it will be run every time the app starts, so use sparingly.+ #' @rdname tdata |
|
| 13 | +35 |
- #'+ #' @export |
|
| 14 | +36 |
- #' Pass this module instead of a `teal_data` object in a call to [init()].+ join_keys.tdata <- function(...) {
|
|
| 15 | -+ | ||
| 37 | +! |
- #' Note that the server function must always return a `teal_data` object wrapped in a reactive expression.+ .deprecate_tdata_msg() |
|
| 16 | +38 |
- #'+ } |
|
| 17 | +39 |
- #' See vignette `vignette("data-as-shiny-module", package = "teal")` for more details.
+
|
|
| 18 | +40 |
- #'+ #' @rdname tdata |
|
| 19 | +41 |
- #' @param ui (`function(id)`)+ #' @export |
|
| 20 | +42 |
- #' `shiny` module UI function; must only take `id` argument+ get_metadata <- function(...) {
|
|
| 21 | -+ | ||
| 43 | +! |
- #' @param server (`function(id)`)+ .deprecate_tdata_msg() |
|
| 22 | +44 |
- #' `shiny` module server function; must only take `id` argument;+ } |
|
| 23 | +45 |
- #' must return reactive expression containing `teal_data` object+ |
|
| 24 | +46 |
- #' @param label (`character(1)`) Label of the module.+ #' @rdname tdata |
|
| 25 | +47 |
- #' @param once (`logical(1)`)+ #' @export |
|
| 26 | +48 |
- #' If `TRUE`, the data module will be shown only once and will disappear after successful data loading.+ as_tdata <- function(...) {
|
|
| 27 | -+ | ||
| 49 | +! |
- #' App user will no longer be able to interact with this module anymore.+ .deprecate_tdata_msg() |
|
| 28 | +50 |
- #' If `FALSE`, the data module can be reused multiple times.+ } |
|
| 29 | +51 |
- #' App user will be able to interact and change the data output from the module multiple times.+ |
|
| 30 | +52 |
- #'+ |
|
| 31 | +53 |
- #' @return+ .deprecate_tdata_msg <- function() {
|
|
| 32 | -+ | ||
| 54 | +! |
- #' `teal_data_module` returns a list of class `teal_data_module` containing two elements, `ui` and+ lifecycle::deprecate_stop( |
|
| 33 | -+ | ||
| 55 | +! |
- #' `server` provided via arguments.+ when = "0.16", |
|
| 34 | -+ | ||
| 56 | +! |
- #'+ what = "tdata()", |
|
| 35 | -+ | ||
| 57 | +! |
- #' @examples+ details = paste( |
|
| 36 | -+ | ||
| 58 | +! |
- #' tdm <- teal_data_module(+ "tdata has been removed in favour of `teal_data`.\n", |
|
| 37 | -+ | ||
| 59 | +! |
- #' ui = function(id) {
+ "Please follow migration instructions https://github.com/insightsengineering/teal/discussions/987." |
|
| 38 | +60 |
- #' ns <- NS(id)+ ) |
|
| 39 | +61 |
- #' actionButton(ns("submit"), label = "Load data")
+ ) |
|
| 40 | +62 |
- #' },+ } |
| 41 | +1 |
- #' server = function(id) {
+ #' Evaluate expression on `teal_data_module` |
||
| 42 | +2 |
- #' moduleServer(id, function(input, output, session) {
+ #' |
||
| 43 | +3 |
- #' eventReactive(input$submit, {
+ #' @details |
||
| 44 | +4 |
- #' data <- within(+ #' `within` is a convenience function for evaluating inline code inside the environment of a `teal_data_module`. |
||
| 45 | +5 |
- #' teal_data(),+ #' It accepts only inline expressions (both simple and compound) and allows for injecting values into `expr` through |
||
| 46 | +6 |
- #' {
+ #' the `...` argument: as `name:value` pairs are passed to `...`, `name` in `expr` will be replaced with `value.` |
||
| 47 | +7 |
- #' dataset1 <- iris+ #' |
||
| 48 | +8 |
- #' dataset2 <- mtcars+ #' @param data (`teal_data_module`) object |
||
| 49 | +9 |
- #' }+ #' @param expr (`expression`) to evaluate. Must be inline code. See [within()] |
||
| 50 | +10 |
- #' )+ #' @param ... See `Details`. |
||
| 51 | +11 |
#' |
||
| 52 | +12 |
- #' data+ #' @return |
||
| 53 | +13 |
- #' })+ #' `within` returns a `teal_data_module` object with a delayed evaluation of `expr` when the module is run. |
||
| 54 | +14 |
- #' })+ #' |
||
| 55 | +15 |
- #' }+ #' @examples |
||
| 56 | +16 |
- #' )+ #' within(tdm, dataset1 <- subset(dataset1, Species == "virginica")) |
||
| 57 | +17 |
#' |
||
| 58 | +18 |
- #' @name teal_data_module+ #' # use additional parameter for expression value substitution. |
||
| 59 | +19 |
- #' @seealso [`teal.data::teal_data-class`], [teal.code::qenv()]+ #' valid_species <- "versicolor" |
||
| 60 | +20 |
- #'+ #' within(tdm, dataset1 <- subset(dataset1, Species %in% species), species = valid_species) |
||
| 61 | +21 |
- #' @export+ #' @include teal_data_module.R |
||
| 62 | +22 |
- teal_data_module <- function(ui, server, label = "data module", once = TRUE) {
+ #' @name within |
||
| 63 | -33x | +|||
| 23 | +
- checkmate::assert_function(ui, args = "id", nargs = 1)+ #' @rdname teal_data_module |
|||
| 64 | -32x | +|||
| 24 | +
- checkmate::assert_function(server, args = "id", nargs = 1)+ #' |
|||
| 65 | -30x | +|||
| 25 | +
- checkmate::assert_string(label)+ #' @export |
|||
| 66 | -30x | +|||
| 26 | +
- checkmate::assert_flag(once)+ #' |
|||
| 67 | -30x | +|||
| 27 | +
- structure(+ within.teal_data_module <- function(data, expr, ...) {
|
|||
| 68 | -30x | +28 | +2x |
- list(+ expr <- substitute(expr) |
| 69 | -30x | +29 | +2x |
- ui = ui,+ extras <- list(...) |
| 70 | -30x | +|||
| 30 | +
- server = function(id) {
+
|
|||
| 71 | -23x | +|||
| 31 | +
- data_out <- server(id)+ # Add braces for consistency. |
|||
| 72 | -22x | +32 | +2x |
- decorate_err_msg(+ if (!identical(as.list(expr)[[1L]], as.symbol("{"))) {
|
| 73 | -22x | +33 | +2x |
- assert_reactive(data_out),+ expr <- call("{", expr)
|
| 74 | -22x | +|||
| 34 | +
- pre = sprintf("From: 'teal_data_module()':\nA 'teal_data_module' with \"%s\" label:", label),
+ } |
|||
| 75 | -22x | +|||
| 35 | +
- post = "Please make sure that this module returns a 'reactive` object containing 'teal_data' class of object." # nolint: line_length_linter.+ |
|||
| 76 | -+ | |||
| 36 | +2x |
- )+ calls <- as.list(expr)[-1] |
||
| 77 | +37 |
- }+ |
||
| 78 | +38 |
- ),+ # Inject extra values into expressions. |
||
| 79 | -30x | +39 | +2x |
- label = label,+ calls <- lapply(calls, function(x) do.call(substitute, list(x, env = extras))) |
| 80 | -30x | +|||
| 40 | +
- class = "teal_data_module",+ |
|||
| 81 | -30x | -
- once = once- |
- ||
| 82 | -+ | 41 | +2x |
- )+ eval_code(object = data, code = as.expression(calls)) |
| 83 | +42 |
}@@ -45999,2165 +45700,2129 @@ teal coverage - 60.11% |
| 1 |
- #' Send input validation messages to output+ .onLoad <- function(libname, pkgname) {
|
||
| 2 |
- #'+ # adapted from https://github.com/r-lib/devtools/blob/master/R/zzz.R |
||
| 3 |
- #' Captures messages from `InputValidator` objects and collates them+ |
||
| 4 | -+ | ! |
- #' into one message passed to `validate`.+ teal_default_options <- list( |
| 5 | -+ | ! |
- #'+ teal.show_js_log = FALSE, |
| 6 | -+ | ! |
- #' `shiny::validate` is used to withhold rendering of an output element until+ teal.lockfile.mode = "auto", |
| 7 | -+ | ! |
- #' certain conditions are met and to print a validation message in place+ shiny.sanitize.errors = FALSE |
| 8 |
- #' of the output element.+ ) |
||
| 9 |
- #' `shinyvalidate::InputValidator` allows to validate input elements+ |
||
| 10 | -+ | ! |
- #' and to display specific messages in their respective input widgets.+ op <- options() |
| 11 | -+ | ! |
- #' `validate_inputs` provides a hybrid solution.+ toset <- !(names(teal_default_options) %in% names(op)) |
| 12 | -+ | ! |
- #' Given an `InputValidator` object, messages corresponding to inputs that fail validation+ if (any(toset)) options(teal_default_options[toset]) |
| 13 |
- #' are extracted and placed in one validation message that is passed to a `validate`/`need` call.+ |
||
| 14 |
- #' This way the input `validator` messages are repeated in the output.+ # Set up the teal logger instance |
||
| 15 | -+ | ! |
- #'+ teal.logger::register_logger("teal")
|
| 16 | -+ | ! |
- #' The `...` argument accepts any number of `InputValidator` objects+ teal.logger::register_handlers("teal")
|
| 17 |
- #' or a nested list of such objects.+ |
||
| 18 | -+ | ! |
- #' If `validators` are passed directly, all their messages are printed together+ invisible() |
| 19 |
- #' under one (optional) header message specified by `header`. If a list is passed,+ } |
||
| 20 |
- #' messages are grouped by `validator`. The list's names are used as headers+ |
||
| 21 |
- #' for their respective message groups.+ .onAttach <- function(libname, pkgname) {
|
||
| 22 | -+ | 2x |
- #' If neither of the nested list elements is named, a header message is taken from `header`.+ packageStartupMessage( |
| 23 | -+ | 2x |
- #'+ "\nYou are using teal version ", |
| 24 |
- #' @param ... either any number of `InputValidator` objects+ # `system.file` uses the `shim` of `system.file` by `teal` |
||
| 25 |
- #' or an optionally named, possibly nested `list` of `InputValidator`+ # we avoid `desc` dependency here to get the version |
||
| 26 | -+ | 2x |
- #' objects, see `Details`+ read.dcf(system.file("DESCRIPTION", package = "teal"))[, "Version"]
|
| 27 |
- #' @param header (`character(1)`) generic validation message; set to NULL to omit+ ) |
||
| 28 |
- #'+ } |
||
| 29 |
- #' @return+ |
||
| 30 |
- #' Returns NULL if the final validation call passes and a `shiny.silent.error` if it fails.+ # This one is here because setdiff_teal_slice should not be exported from teal.slice. |
||
| 31 |
- #'+ setdiff_teal_slices <- getFromNamespace("setdiff_teal_slices", "teal.slice")
|
||
| 32 |
- #' @seealso [`shinyvalidate::InputValidator`], [`shiny::validate`]+ # This one is here because it is needed by c.teal_slices but we don't want it exported from teal.slice. |
||
| 33 |
- #'+ coalesce_r <- getFromNamespace("coalesce_r", "teal.slice")
|
||
| 34 |
- #' @examplesIf require("shinyvalidate")
+ # all *Block objects are private in teal.reporter |
||
| 35 |
- #' library(shiny)+ RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter") # nolint: object_name.
|
||
| 36 |
- #' library(shinyvalidate)+ |
||
| 37 |
- #'+ # Use non-exported function(s) from teal.code |
||
| 38 |
- #' ui <- fluidPage(+ # This one is here because lang2calls should not be exported from teal.code |
||
| 39 |
- #' selectInput("method", "validation method", c("sequential", "combined", "grouped")),
+ lang2calls <- getFromNamespace("lang2calls", "teal.code")
|
||
| 40 |
- #' sidebarLayout(+ code2list <- getFromNamespace("code2list", "teal.data")
|
| 41 | +1 |
- #' sidebarPanel(+ #' Check that argument is reactive. |
|
| 42 | +2 |
- #' selectInput("letter", "select a letter:", c(letters[1:3], LETTERS[4:6])),
+ #' |
|
| 43 | +3 |
- #' selectInput("number", "select a number:", 1:6),
+ #' @inherit checkmate::check_class params return |
|
| 44 | +4 |
- #' tags$br(),+ #' |
|
| 45 | +5 |
- #' selectInput("color", "select a color:",
+ #' @keywords internal |
|
| 46 | +6 |
- #' c("black", "indianred2", "springgreen2", "cornflowerblue"),
+ check_reactive <- function(x, null.ok = FALSE) { # nolint: object_name_linter.
|
|
| 47 | -+ | ||
| 7 | +1134x |
- #' multiple = TRUE+ if (!isTRUE(checkmate::test_class(x, classes = "reactive", null.ok = null.ok))) {
|
|
| 48 | -+ | ||
| 8 | +4x |
- #' ),+ cl <- class(x) |
|
| 49 | -+ | ||
| 9 | +4x |
- #' sliderInput("size", "select point size:",
+ return(sprintf( |
|
| 50 | -+ | ||
| 10 | +4x |
- #' min = 0.1, max = 4, value = 0.25+ "Must be a reactive (i.e. inherit from 'reactive' class) but has class%s '%s'", |
|
| 51 | -+ | ||
| 11 | +4x |
- #' )+ if (length(cl) > 1L) "es" else "", |
|
| 52 | -+ | ||
| 12 | +4x |
- #' ),+ paste0(cl, collapse = "','") |
|
| 53 | +13 |
- #' mainPanel(plotOutput("plot"))
+ )) |
|
| 54 | +14 |
- #' )+ } |
|
| 55 | -+ | ||
| 15 | +1130x |
- #' )+ return(TRUE) |
|
| 56 | +16 |
- #'+ } |
|
| 57 | +17 |
- #' server <- function(input, output) {
+ #' @rdname check_reactive |
|
| 58 | +18 |
- #' # set up input validation+ test_reactive <- function(x, null.ok = FALSE) { # nolint: object_name_linter.
|
|
| 59 | -+ | ||
| 19 | +30x |
- #' iv <- InputValidator$new()+ isTRUE(check_reactive(x, null.ok = null.ok)) |
|
| 60 | +20 |
- #' iv$add_rule("letter", sv_in_set(LETTERS, "choose a capital letter"))
+ } |
|
| 61 | +21 |
- #' iv$add_rule("number", function(x) {
+ #' @rdname check_reactive |
|
| 62 | +22 |
- #' if (as.integer(x) %% 2L == 1L) "choose an even number"+ assert_reactive <- checkmate::makeAssertionFunction(check_reactive) |
|
| 63 | +23 |
- #' })+ |
|
| 64 | +24 |
- #' iv$enable()+ #' Capture error and decorate error message. |
|
| 65 | +25 |
- #' # more input validation+ #' |
|
| 66 | +26 |
- #' iv_par <- InputValidator$new()+ #' @param x object to evaluate |
|
| 67 | +27 |
- #' iv_par$add_rule("color", sv_required(message = "choose a color"))
+ #' @param pre (`character(1)`) A string to prepend to error message |
|
| 68 | +28 |
- #' iv_par$add_rule("color", function(x) {
+ #' @param post (`character(1)`) A string to append to error message |
|
| 69 | +29 |
- #' if (length(x) > 1L) "choose only one color"+ #' |
|
| 70 | +30 |
- #' })+ #' @return `x` if no error, otherwise throws error with decorated message |
|
| 71 | +31 |
- #' iv_par$add_rule(+ #' |
|
| 72 | +32 |
- #' "size",+ #' @keywords internal |
|
| 73 | +33 |
- #' sv_between(+ decorate_err_msg <- function(x, pre = character(0), post = character(0)) {
|
|
| 74 | -+ | ||
| 34 | +47x |
- #' left = 0.5, right = 3,+ tryCatch( |
|
| 75 | -+ | ||
| 35 | +47x |
- #' message_fmt = "choose a value between {left} and {right}"
+ x, |
|
| 76 | -+ | ||
| 36 | +47x |
- #' )+ error = function(e) {
|
|
| 77 | -+ | ||
| 37 | +2x |
- #' )+ stop( |
|
| 78 | -+ | ||
| 38 | +2x |
- #' iv_par$enable()+ "\n", |
|
| 79 | -+ | ||
| 39 | +2x |
- #'+ pre, |
|
| 80 | -+ | ||
| 40 | +2x |
- #' output$plot <- renderPlot({
+ "\n", |
|
| 81 | -+ | ||
| 41 | +2x |
- #' # validate output+ e$message, |
|
| 82 | -+ | ||
| 42 | +2x |
- #' switch(input[["method"]],+ "\n",+ |
+ |
| 43 | +2x | +
+ post,+ |
+ |
| 44 | +2x | +
+ call. = FALSE |
|
| 83 | +45 |
- #' "sequential" = {
+ ) |
|
| 84 | +46 |
- #' validate_inputs(iv)+ } |
|
| 85 | +47 |
- #' validate_inputs(iv_par, header = "Set proper graphical parameters")+ )+ |
+ |
| 48 | +45x | +
+ x |
|
| 86 | +49 |
- #' },+ } |
| 87 | +1 |
- #' "combined" = validate_inputs(iv, iv_par),+ #' Filter settings for `teal` applications |
||
| 88 | +2 |
- #' "grouped" = validate_inputs(list(+ #' |
||
| 89 | +3 |
- #' "Some inputs require attention" = iv,+ #' Specify initial filter states and filtering settings for a `teal` app. |
||
| 90 | +4 |
- #' "Set proper graphical parameters" = iv_par+ #' |
||
| 91 | +5 |
- #' ))+ #' Produces a `teal_slices` object. |
||
| 92 | +6 |
- #' )+ #' The `teal_slice` components will specify filter states that will be active when the app starts. |
||
| 93 | +7 |
- #'+ #' Attributes (created with the named arguments) will configure the way the app applies filters. |
||
| 94 | +8 |
- #' plot(faithful$eruptions ~ faithful$waiting,+ #' See argument descriptions for details. |
||
| 95 | +9 |
- #' las = 1, pch = 16,+ #' |
||
| 96 | +10 |
- #' col = input[["color"]], cex = input[["size"]]+ #' @inheritParams teal.slice::teal_slices |
||
| 97 | +11 |
- #' )+ #' |
||
| 98 | +12 |
- #' })+ #' @param module_specific (`logical(1)`) optional, |
||
| 99 | +13 |
- #' }+ #' - `FALSE` (default) when one filter panel applied to all modules. |
||
| 100 | +14 |
- #'+ #' All filters will be shared by all modules. |
||
| 101 | +15 |
- #' if (interactive()) {
+ #' - `TRUE` when filter panel module-specific. |
||
| 102 | +16 |
- #' shinyApp(ui, server)+ #' Modules can have different set of filters specified - see `mapping` argument. |
||
| 103 | +17 |
- #' }+ #' @param mapping `r lifecycle::badge("experimental")`
|
||
| 104 | +18 |
- #'+ #' _This is a new feature. Do kindly share your opinions on |
||
| 105 | +19 |
- #' @export+ #' [`teal`'s GitHub repository](https://github.com/insightsengineering/teal/)._ |
||
| 106 | +20 |
#' |
||
| 107 | +21 |
- validate_inputs <- function(..., header = "Some inputs require attention") {
+ #' (named `list`) specifies which filters will be active in which modules on app start. |
||
| 108 | -36x | +|||
| 22 | +
- dots <- list(...)+ #' Elements should contain character vector of `teal_slice` `id`s (see [`teal.slice::teal_slice`]). |
|||
| 109 | -2x | +|||
| 23 | +
- if (!is_validators(dots)) stop("validate_inputs accepts validators or a list thereof")
+ #' Names of the list should correspond to `teal_module` `label` set in [module()] function. |
|||
| 110 | +24 |
-
+ #' - `id`s listed under `"global_filters` will be active in all modules. |
||
| 111 | -34x | +|||
| 25 | +
- messages <- extract_validator(dots, header)+ #' - If missing, all filters will be applied to all modules. |
|||
| 112 | -34x | +|||
| 26 | +
- failings <- if (!any_names(dots)) {
+ #' - If empty list, all filters will be available to all modules but will start inactive. |
|||
| 113 | -29x | +|||
| 27 | +
- add_header(messages, header)+ #' - If `module_specific` is `FALSE`, only `global_filters` will be active on start. |
|||
| 114 | +28 |
- } else {
+ #' @param app_id (`character(1)`) |
||
| 115 | -5x | +|||
| 29 | +
- unlist(messages)+ #' For internal use only, do not set manually. |
|||
| 116 | +30 |
- }+ #' Added by `init` so that a `teal_slices` can be matched to the app in which it was used. |
||
| 117 | +31 |
-
+ #' Used for verifying snapshots uploaded from file. See `snapshot`. |
||
| 118 | -34x | +|||
| 32 | +
- shiny::validate(shiny::need(is.null(failings), failings))+ #' |
|||
| 119 | +33 |
- }+ #' @param x (`list`) of lists to convert to `teal_slices` |
||
| 120 | +34 |
-
+ #' |
||
| 121 | +35 |
- ### internal functions+ #' @return |
||
| 122 | +36 |
-
+ #' A `teal_slices` object. |
||
| 123 | +37 |
- #' @noRd+ #' |
||
| 124 | +38 |
- #' @keywords internal+ #' @seealso [`teal.slice::teal_slices`], [`teal.slice::teal_slice`], [slices_store()] |
||
| 125 | +39 |
- # recursive object type test+ #' |
||
| 126 | +40 |
- # returns logical of length 1+ #' @examples |
||
| 127 | +41 |
- is_validators <- function(x) {
+ #' filter <- teal_slices( |
||
| 128 | -118x | +|||
| 42 | +
- all(if (is.list(x)) unlist(lapply(x, is_validators)) else inherits(x, "InputValidator"))+ #' teal_slice(dataname = "iris", varname = "Species", id = "species"), |
|||
| 129 | +43 |
- }+ #' teal_slice(dataname = "iris", varname = "Sepal.Length", id = "sepal_length"), |
||
| 130 | +44 |
-
+ #' teal_slice( |
||
| 131 | +45 |
- #' @noRd+ #' dataname = "iris", id = "long_petals", title = "Long petals", expr = "Petal.Length > 5" |
||
| 132 | +46 |
- #' @keywords internal+ #' ), |
||
| 133 | +47 |
- # test if an InputValidator object is enabled+ #' teal_slice(dataname = "mtcars", varname = "mpg", id = "mtcars_mpg"), |
||
| 134 | +48 |
- # returns logical of length 1+ #' mapping = list( |
||
| 135 | +49 |
- # official method requested at https://github.com/rstudio/shinyvalidate/issues/64+ #' module1 = c("species", "sepal_length"),
|
||
| 136 | +50 |
- validator_enabled <- function(x) {
+ #' module2 = c("mtcars_mpg"),
|
||
| 137 | -49x | +|||
| 51 | +
- x$.__enclos_env__$private$enabled+ #' global_filters = "long_petals" |
|||
| 138 | +52 |
- }+ #' ) |
||
| 139 | +53 |
-
+ #' ) |
||
| 140 | +54 |
- #' Recursively extract messages from validator list+ #' |
||
| 141 | +55 |
- #' @return A character vector or a list of character vectors, possibly nested and named.+ #' app <- init( |
||
| 142 | +56 |
- #' @noRd+ #' data = teal_data(iris = iris, mtcars = mtcars), |
||
| 143 | +57 |
- #' @keywords internal+ #' modules = list( |
||
| 144 | +58 |
- extract_validator <- function(iv, header) {
+ #' module("module1"),
|
||
| 145 | -113x | +|||
| 59 | +
- if (inherits(iv, "InputValidator")) {
+ #' module("module2")
|
|||
| 146 | -49x | +|||
| 60 | +
- add_header(gather_messages(iv), header)+ #' ), |
|||
| 147 | +61 |
- } else {
+ #' filter = filter |
||
| 148 | -58x | +|||
| 62 | +
- if (is.null(names(iv))) names(iv) <- rep("", length(iv))
+ #' ) |
|||
| 149 | -64x | +|||
| 63 | +
- mapply(extract_validator, iv = iv, header = names(iv), SIMPLIFY = FALSE)+ #' |
|||
| 150 | +64 |
- }+ #' if (interactive()) {
|
||
| 151 | +65 |
- }+ #' shinyApp(app$ui, app$server) |
||
| 152 | +66 |
-
+ #' } |
||
| 153 | +67 |
- #' Collate failing messages from validator.+ #' |
||
| 154 | +68 |
- #' @return `list`+ #' @export |
||
| 155 | +69 |
- #' @noRd+ teal_slices <- function(..., |
||
| 156 | +70 |
- #' @keywords internal+ exclude_varnames = NULL, |
||
| 157 | +71 |
- gather_messages <- function(iv) {
+ include_varnames = NULL, |
||
| 158 | -49x | +|||
| 72 | +
- if (validator_enabled(iv)) {
+ count_type = NULL, |
|||
| 159 | -46x | +|||
| 73 | +
- status <- iv$validate()+ allow_add = TRUE, |
|||
| 160 | -46x | +|||
| 74 | +
- failing_inputs <- Filter(Negate(is.null), status)+ module_specific = FALSE, |
|||
| 161 | -46x | +|||
| 75 | +
- unique(lapply(failing_inputs, function(x) x[["message"]]))+ mapping, |
|||
| 162 | +76 |
- } else {
+ app_id = NULL) {
|
||
| 163 | -3x | +77 | +170x |
- warning("Validator is disabled and will be omitted.")
+ shiny::isolate({
|
| 164 | -3x | +78 | +170x |
- list()+ checkmate::assert_flag(allow_add) |
| 165 | -+ | |||
| 79 | +170x |
- }+ checkmate::assert_flag(module_specific) |
||
| 166 | -+ | |||
| 80 | +53x |
- }+ if (!missing(mapping)) checkmate::assert_list(mapping, types = c("character", "NULL"), names = "named")
|
||
| 167 | -+ | |||
| 81 | +167x |
-
+ checkmate::assert_string(app_id, null.ok = TRUE) |
||
| 168 | +82 |
- #' Add optional header to failing messages+ |
||
| 169 | -+ | |||
| 83 | +167x |
- #' @noRd+ slices <- list(...) |
||
| 170 | -+ | |||
| 84 | +167x |
- #' @keywords internal+ all_slice_id <- vapply(slices, `[[`, character(1L), "id") |
||
| 171 | +85 |
- add_header <- function(messages, header = "") {
+
|
||
| 172 | -78x | +86 | +167x |
- ans <- unlist(messages)+ if (missing(mapping)) {
|
| 173 | -78x | +87 | +117x |
- if (length(ans) != 0L && isTRUE(nchar(header) > 0L)) {
+ mapping <- if (length(all_slice_id)) {
|
| 174 | -31x | +88 | +26x |
- ans <- c(paste0(header, "\n"), ans, "\n")+ list(global_filters = all_slice_id) |
| 175 | +89 |
- }+ } else {
|
||
| 176 | -78x | +90 | +91x |
- ans+ list() |
| 177 | +91 |
- }+ } |
||
| 178 | +92 |
-
+ } |
||
| 179 | +93 |
- #' Recursively check if the object contains a named list+ |
||
| 180 | -+ | |||
| 94 | +167x |
- #' @noRd+ if (!module_specific) {
+ |
+ ||
| 95 | +148x | +
+ mapping[setdiff(names(mapping), "global_filters")] <- NULL |
||
| 181 | +96 |
- #' @keywords internal+ } |
||
| 182 | +97 |
- any_names <- function(x) {
+
|
||
| 183 | -103x | +98 | +167x |
- any(+ failed_slice_id <- setdiff(unlist(mapping), all_slice_id) |
| 184 | -103x | +99 | +167x |
- if (is.list(x)) {
+ if (length(failed_slice_id)) {
|
| 185 | -58x | +100 | +1x |
- if (!is.null(names(x)) && any(names(x) != "")) TRUE else unlist(lapply(x, any_names))+ stop(sprintf( |
| 186 | -+ | |||
| 101 | +1x |
- } else {
+ "Filters in mapping don't match any available filter.\n %s not in %s", |
||
| 187 | -40x | +102 | +1x |
- FALSE+ toString(failed_slice_id), |
| 188 | -+ | |||
| 103 | +1x |
- }+ toString(all_slice_id) |
||
| 189 | +104 |
- )+ )) |
||
| 190 | +105 |
- }+ } |
| 1 | +106 |
- #' Check that argument is reactive.+ |
||
| 2 | -+ | |||
| 107 | +166x |
- #'+ tss <- teal.slice::teal_slices( |
||
| 3 | +108 |
- #' @inherit checkmate::check_class params return+ ..., |
||
| 4 | -+ | |||
| 109 | +166x |
- #'+ exclude_varnames = exclude_varnames, |
||
| 5 | -+ | |||
| 110 | +166x |
- #' @keywords internal+ include_varnames = include_varnames, |
||
| 6 | -+ | |||
| 111 | +166x |
- check_reactive <- function(x, null.ok = FALSE) { # nolint: object_name_linter.
+ count_type = count_type, |
||
| 7 | -1054x | +112 | +166x |
- if (!isTRUE(checkmate::test_class(x, classes = "reactive", null.ok = null.ok))) {
+ allow_add = allow_add+ |
+
| 113 | ++ |
+ ) |
||
| 8 | -4x | +114 | +166x |
- cl <- class(x)+ attr(tss, "mapping") <- mapping |
| 9 | -4x | +115 | +166x |
- return(sprintf(+ attr(tss, "module_specific") <- module_specific |
| 10 | -4x | +116 | +166x |
- "Must be a reactive (i.e. inherit from 'reactive' class) but has class%s '%s'",+ attr(tss, "app_id") <- app_id |
| 11 | -4x | +117 | +166x |
- if (length(cl) > 1L) "es" else "",+ class(tss) <- c("modules_teal_slices", class(tss))
|
| 12 | -4x | +118 | +166x |
- paste0(cl, collapse = "','")+ tss |
| 13 | +119 |
- ))+ }) |
||
| 14 | +120 |
- }+ } |
||
| 15 | -1050x | +|||
| 121 | +
- return(TRUE)+ |
|||
| 16 | +122 |
- }+ |
||
| 17 | +123 |
- #' @rdname check_reactive+ #' @rdname teal_slices |
||
| 18 | +124 |
- test_reactive <- function(x, null.ok = FALSE) { # nolint: object_name_linter.
+ #' @export |
||
| 19 | -30x | +|||
| 125 | +
- isTRUE(check_reactive(x, null.ok = null.ok))+ #' @keywords internal |
|||
| 20 | +126 |
- }+ #' |
||
| 21 | +127 |
- #' @rdname check_reactive+ as.teal_slices <- function(x) { # nolint: object_name.
|
||
| 22 | -+ | |||
| 128 | +15x |
- assert_reactive <- checkmate::makeAssertionFunction(check_reactive)+ checkmate::assert_list(x)+ |
+ ||
| 129 | +15x | +
+ lapply(x, checkmate::assert_list, names = "named", .var.name = "list element") |
||
| 23 | +130 | |||
| 24 | -+ | |||
| 131 | +15x |
- #' Capture error and decorate error message.+ attrs <- attributes(unclass(x)) |
||
| 25 | -+ | |||
| 132 | +15x |
- #'+ ans <- lapply(x, function(x) if (is.teal_slice(x)) x else as.teal_slice(x))+ |
+ ||
| 133 | +15x | +
+ do.call(teal_slices, c(ans, attrs)) |
||
| 26 | +134 |
- #' @param x object to evaluate+ } |
||
| 27 | +135 |
- #' @param pre (`character(1)`) A string to prepend to error message+ |
||
| 28 | +136 |
- #' @param post (`character(1)`) A string to append to error message+ |
||
| 29 | +137 |
- #'+ #' @rdname teal_slices |
||
| 30 | +138 |
- #' @return `x` if no error, otherwise throws error with decorated message+ #' @export |
||
| 31 | +139 |
- #'+ #' @keywords internal |
||
| 32 | +140 |
- #' @keywords internal+ #' |
||
| 33 | +141 |
- decorate_err_msg <- function(x, pre = character(0), post = character(0)) {
+ c.teal_slices <- function(...) {
|
||
| 34 | -47x | +142 | +6x |
- tryCatch(+ x <- list(...) |
| 35 | -47x | +143 | +6x |
- x,+ checkmate::assert_true(all(vapply(x, is.teal_slices, logical(1L))), .var.name = "all arguments are teal_slices") |
| 36 | -47x | +|||
| 144 | +
- error = function(e) {
+
|
|||
| 37 | -2x | +145 | +6x |
- stop(+ all_attributes <- lapply(x, attributes) |
| 38 | -2x | +146 | +6x |
- "\n",+ all_attributes <- coalesce_r(all_attributes) |
| 39 | -2x | +147 | +6x |
- pre,+ all_attributes <- all_attributes[names(all_attributes) != "class"] |
| 40 | -2x | +|||
| 148 | +
- "\n",+ |
|||
| 41 | -2x | +149 | +6x |
- e$message,+ do.call( |
| 42 | -2x | +150 | +6x |
- "\n",+ teal_slices, |
| 43 | -2x | +151 | +6x |
- post,+ c( |
| 44 | -2x | +152 | +6x |
- call. = FALSE+ unique(unlist(x, recursive = FALSE)), |
| 45 | -+ | |||
| 153 | +6x |
- )+ all_attributes |
||
| 46 | +154 |
- }+ ) |
||
| 47 | +155 |
) |
||
| 48 | -45x | -
- x- |
- ||
| 49 | +156 |
} |
| 1 | +157 |
- #' Store and restore `teal_slices` object+ |
|
| 2 | +158 |
- #'+ |
|
| 3 | +159 |
- #' Functions that write a `teal_slices` object to a file in the `JSON` format,+ #' Deep copy `teal_slices` |
|
| 4 | +160 |
- #' and also restore the object from disk.+ #' |
|
| 5 | +161 |
- #'+ #' it's important to create a new copy of `teal_slices` when |
|
| 6 | +162 |
- #' Date and date time objects are stored in the following formats:+ #' starting a new `shiny` session. Otherwise, object will be shared |
|
| 7 | +163 |
- #'+ #' by multiple users as it is created in global environment before |
|
| 8 | +164 |
- #' - `Date` class is converted to the `"ISO8601"` standard (`YYYY-MM-DD`).+ #' `shiny` session starts. |
|
| 9 | +165 |
- #' - `POSIX*t` classes are converted to character by using+ #' @param filter (`teal_slices`) |
|
| 10 | +166 |
- #' `format.POSIX*t(usetz = TRUE, tz = "UTC")` (`YYYY-MM-DD HH:MM:SS UTC`, where+ #' @return `teal_slices` |
|
| 11 | +167 |
- #' `UTC` is the `Coordinated Universal Time` timezone short-code).+ #' @keywords internal |
|
| 12 | +168 |
- #'+ deep_copy_filter <- function(filter) {
|
|
| 13 | -+ | ||
| 169 | +1x |
- #' This format is assumed during `slices_restore`. All `POSIX*t` objects in+ checkmate::assert_class(filter, "teal_slices") |
|
| 14 | -+ | ||
| 170 | +1x |
- #' `selected` or `choices` fields of `teal_slice` objects are always printed in+ shiny::isolate({
|
|
| 15 | -+ | ||
| 171 | +1x |
- #' `UTC` timezone as well.+ filter_copy <- lapply(filter, function(slice) {
|
|
| 16 | -+ | ||
| 172 | +2x |
- #'+ teal.slice::as.teal_slice(as.list(slice)) |
|
| 17 | +173 |
- #' @param tss (`teal_slices`) object to be stored.+ }) |
|
| 18 | -+ | ||
| 174 | +1x |
- #' @param file (`character(1)`) file path where `teal_slices` object will be+ attributes(filter_copy) <- attributes(filter) |
|
| 19 | -+ | ||
| 175 | +1x |
- #' saved and restored. The file extension should be `".json"`.+ filter_copy |
|
| 20 | +176 |
- #'+ }) |
|
| 21 | +177 |
- #' @return `slices_store` returns `NULL`, invisibly.+ } |
| 22 | +1 |
- #'+ #' `teal_data` utils |
||
| 23 | +2 |
- #' @seealso [teal_slices()]+ #' |
||
| 24 | +3 |
- #'+ #' In `teal` we need to recreate the `teal_data` object due to two operations: |
||
| 25 | +4 |
- #' @keywords internal+ #' - we need to append filter-data code and objects which have been evaluated in `FilteredData` and |
||
| 26 | +5 |
- #'+ #' we want to avoid double-evaluation. |
||
| 27 | +6 |
- slices_store <- function(tss, file) {
+ #' - we need to subset `teal_data` to `datanames` used by the module, to shorten obtainable R-code |
||
| 28 | -9x | +|||
| 7 | +
- checkmate::assert_class(tss, "teal_slices")+ #' |
|||
| 29 | -9x | +|||
| 8 | +
- checkmate::assert_path_for_output(file, overwrite = TRUE, extension = "json")+ #' Due to above recreation of `teal_data` object can't be done simply by using public |
|||
| 30 | +9 |
-
+ #' `teal.code` and `teal.data` methods. |
||
| 31 | -9x | +|||
| 10 | +
- cat(format(tss, trim_lines = FALSE), "\n", file = file)+ #' |
|||
| 32 | +11 |
- }+ #' @param data (`teal_data`) |
||
| 33 | +12 |
-
+ #' @param code (`character`) code to append to the object's code slot. |
||
| 34 | +13 |
- #' @rdname slices_store+ #' @param objects (`list`) objects to append to object's environment. |
||
| 35 | +14 |
- #' @return `slices_restore` returns a `teal_slices` object restored from the file.+ #' @return modified `teal_data` |
||
| 36 | +15 |
#' @keywords internal |
||
| 37 | +16 |
- slices_restore <- function(file) {
- |
- ||
| 38 | -9x | -
- checkmate::assert_file_exists(file, access = "r", extension = "json")+ #' @name teal_data_utilities |
||
| 39 | +17 | - - | -||
| 40 | -9x | -
- tss_json <- jsonlite::fromJSON(file, simplifyDataFrame = FALSE)- |
- ||
| 41 | -9x | -
- tss_json$slices <-- |
- ||
| 42 | -9x | -
- lapply(tss_json$slices, function(slice) {
- |
- ||
| 43 | -9x | -
- for (field in c("selected", "choices")) {
- |
- ||
| 44 | -18x | -
- if (!is.null(slice[[field]])) {
- |
- ||
| 45 | -12x | -
- if (length(slice[[field]]) > 0) {
- |
- ||
| 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$")
+ NULL |
||
| 48 | +18 | |||
| 49 | -9x | +|||
| 19 | +
- slice[[field]] <-+ #' @rdname teal_data_utilities |
|||
| 50 | -9x | +|||
| 20 | +
- if (all(grepl(paste0(date_partial_regex, "$"), slice[[field]]))) {
+ .append_evaluated_code <- function(data, code) {
|
|||
| 51 | -3x | +21 | +89x |
- as.Date(slice[[field]])+ checkmate::assert_class(data, "teal_data") |
| 52 | -9x | +22 | +89x |
- } else if (all(grepl(time_stamp_regex, slice[[field]]))) {
+ data@code <- c(data@code, code2list(code)) |
| 53 | -3x | -
- as.POSIXct(slice[[field]], tz = "UTC")- |
- ||
| 54 | -+ | 23 | +89x |
- } else {
+ methods::validObject(data) |
| 55 | -3x | -
- slice[[field]]- |
- ||
| 56 | -+ | 24 | +89x |
- }+ data |
| 57 | +25 |
- } else {
- |
- ||
| 58 | -3x | -
- slice[[field]] <- character(0)+ } |
||
| 59 | +26 |
- }+ |
||
| 60 | +27 |
- }+ #' @rdname teal_data_utilities |
||
| 61 | +28 |
- }+ .append_modified_data <- function(data, objects) {
|
||
| 62 | -9x | +29 | +89x |
- slice+ checkmate::assert_class(data, "teal_data") |
| 63 | -+ | |||
| 30 | +89x |
- })+ checkmate::assert_class(objects, "list") |
||
| 64 | -+ | |||
| 31 | +89x |
-
+ new_env <- list2env(objects, parent = .GlobalEnv) |
||
| 65 | -9x | +32 | +89x |
- tss_elements <- lapply(tss_json$slices, as.teal_slice)+ rlang::env_coalesce(new_env, as.environment(data)) |
| 66 | -+ | |||
| 33 | +89x |
-
+ data@.xData <- new_env |
||
| 67 | -9x | +34 | +89x |
- do.call(teal_slices, c(tss_elements, tss_json$attributes))+ data |
| 68 | +35 |
}@@ -48166,196 +47831,196 @@ teal coverage - 60.11% |
| 1 |
- .onLoad <- function(libname, pkgname) {
+ #' UI and server modules of `teal` |
||
| 2 |
- # adapted from https://github.com/r-lib/devtools/blob/master/R/zzz.R+ #' |
||
| 3 |
-
+ #' @description `r lifecycle::badge("deprecated")`
|
||
| 4 | -! | +
- teal_default_options <- list(+ #' Please use [`module_teal`] instead. |
|
| 5 | -! | +
- teal.show_js_log = FALSE,+ #' |
|
| 6 | -! | +
- teal.lockfile.mode = "auto",+ #' @inheritParams ui_teal |
|
| 7 | -! | +
- shiny.sanitize.errors = FALSE+ #' @inheritParams srv_teal |
|
| 8 |
- )+ #' |
||
| 9 |
-
+ #' @return |
||
| 10 | -! | +
- op <- options()+ #' Returns a `reactive` expression containing a `teal_data` object when data is loaded or `NULL` when it is not. |
|
| 11 | -! | +
- toset <- !(names(teal_default_options) %in% names(op))+ #' @name module_teal_with_splash |
|
| 12 | -! | +
- if (any(toset)) options(teal_default_options[toset])+ #' |
|
| 13 |
-
+ NULL |
||
| 14 |
- # Set up the teal logger instance+ |
||
| 15 | -! | +
- teal.logger::register_logger("teal")
+ #' @export |
|
| 16 | -! | +
- teal.logger::register_handlers("teal")
+ #' @rdname module_teal_with_splash |
|
| 17 |
-
+ ui_teal_with_splash <- function(id, |
||
| 18 | -! | +
- invisible()+ data, |
|
| 19 |
- }+ title = build_app_title(), |
||
| 20 |
-
+ header = tags$p(), |
||
| 21 |
- .onAttach <- function(libname, pkgname) {
+ footer = tags$p()) {
|
||
| 22 | -2x | +! |
- packageStartupMessage(+ lifecycle::deprecate_soft( |
| 23 | -2x | +! |
- "\nYou are using teal version ",+ when = "0.16", |
| 24 | -+ | ! |
- # `system.file` uses the `shim` of `system.file` by `teal`+ what = "ui_teal_with_splash()", |
| 25 | -+ | ! |
- # we avoid `desc` dependency here to get the version+ details = "Deprecated, please use `ui_teal` instead" |
| 26 | -2x | +
- read.dcf(system.file("DESCRIPTION", package = "teal"))[, "Version"]
+ ) |
|
| 27 | -+ | ! |
- )+ ui_teal(id = id, title = title, header = header, footer = footer) |
| 30 |
- # This one is here because setdiff_teal_slice should not be exported from teal.slice.+ #' @export |
||
| 31 |
- setdiff_teal_slices <- getFromNamespace("setdiff_teal_slices", "teal.slice")
+ #' @rdname module_teal_with_splash |
||
| 32 |
- # This one is here because it is needed by c.teal_slices but we don't want it exported from teal.slice.+ srv_teal_with_splash <- function(id, data, modules, filter = teal_slices()) {
|
||
| 33 | -+ | ! |
- coalesce_r <- getFromNamespace("coalesce_r", "teal.slice")
+ lifecycle::deprecate_soft( |
| 34 | -+ | ! |
- # all *Block objects are private in teal.reporter+ when = "0.16", |
| 35 | -+ | ! |
- RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter") # nolint: object_name.
+ what = "srv_teal_with_splash()", |
| 36 | -+ | ! |
-
+ details = "Deprecated, please use `srv_teal` instead" |
| 37 |
- # Use non-exported function(s) from teal.code+ ) |
||
| 38 | -+ | ! |
- # This one is here because lang2calls should not be exported from teal.code+ srv_teal(id = id, data = data, modules = modules, filter = filter) |
| 39 |
- lang2calls <- getFromNamespace("lang2calls", "teal.code")
- |
- ||
| 40 | -- |
- code2list <- getFromNamespace("code2list", "teal.data")
+ } |
49 |
- #' not work with `devtools`. Therefore, we redefine this method in each package+ #' not work with `devtools`. Therefore, we redefine this method in each package+ |
+
+
| 50 | ++ |
+ #' as needed. Thus, we do not export this method.+ |
+ |
| 51 | ++ |
+ #'+ |
+ |
| 52 | ++ |
+ #' @param files (`character`) vector of filenames.+ |
+ |
| 53 | ++ |
+ #'+ |
+ |
| 54 | ++ |
+ #' @return `NULL`, invisibly.+ |
+ |
| 55 | ++ |
+ #' @keywords internal+ |
+ |
| 56 | ++ |
+ run_js_files <- function(files) {
+ |
+ |
| 57 | +88x | +
+ checkmate::assert_character(files, min.len = 1, any.missing = FALSE)+ |
+ |
| 58 | +88x | +
+ lapply(files, function(file) {
+ |
+ |
| 59 | +88x | +
+ shinyjs::runjs(paste0(readLines(system.file("js", file, package = "teal", mustWork = TRUE)), collapse = "\n"))
+ |
+ |
| 60 | ++ |
+ })+ |
+ |
| 61 | +88x | +
+ invisible(NULL)+ |
+ |
| 62 | ++ |
+ }+ |
+ |
| 63 | ++ | + + | +|
| 64 | ++ |
+ #' Code to include `teal` `CSS` and `JavaScript` files+ |
+ |
| 65 | ++ |
+ #'+ |
+ |
| 66 | ++ |
+ #' This is useful when you want to use the same `JavaScript` and `CSS` files that are+ |
+ |
| 67 | ++ |
+ #' used with the `teal` application.+ |
+ |
| 68 | ++ |
+ #' This is also useful for running standalone modules in `teal` with the correct+ |
+ |
| 69 | ++ |
+ #' styles.+ |
+ |
| 70 | ++ |
+ #' Also initializes `shinyjs` so you can use it.+ |
+ |
| 71 | ++ |
+ #'+ |
+ |
| 72 | ++ |
+ #' Simply add `include_teal_css_js()` as one of the UI elements.+ |
+ |
| 73 | ++ |
+ #' @return A `shiny.tag.list`.+ |
+ |
| 74 | ++ |
+ #' @keywords internal+ |
+ |
| 75 | ++ |
+ include_teal_css_js <- function() {
+ |
+ |
| 76 | +! | +
+ tagList(+ |
+ |
| 77 | +! | +
+ shinyjs::useShinyjs(),+ |
+ |
| 78 | +! | +
+ include_css_files(),+ |
+ |
| 79 | ++ |
+ # init.js is executed from the server+ |
+ |
| 80 | +! | +
+ include_js_files(except = "init.js"),+ |
+ |
| 81 | +! | +
+ shinyjs::hidden(icon("fas fa-gear")), # add hidden icon to load font-awesome css for icons
+ |
+ |
| 82 | ++ |
+ )+ |
+ |
| 83 | ++ |
+ }+ |
+
| 1 | ++ |
+ #' Create a `teal` module for previewing a report+ |
+ ||
| 2 | ++ |
+ #'+ |
+ ||
| 3 | ++ |
+ #' @description `r lifecycle::badge("experimental")`
+ |
+ ||
| 4 | ++ |
+ #'+ |
+ ||
| 5 | ++ |
+ #' This function wraps [teal.reporter::reporter_previewer_ui()] and+ |
+ ||
| 6 | ++ |
+ #' [teal.reporter::reporter_previewer_srv()] into a `teal_module` to be+ |
+ ||
| 7 | ++ |
+ #' used in `teal` applications.+ |
+ ||
| 8 | ++ |
+ #'+ |
+ ||
| 9 | ++ |
+ #' If you are creating a `teal` application using [init()] then this+ |
+ ||
| 10 | ++ |
+ #' module will be added to your application automatically if any of your `teal_modules`+ |
+ ||
| 11 | ++ |
+ #' support report generation.+ |
+ ||
| 12 | ++ |
+ #'+ |
+ ||
| 13 | ++ |
+ #' @inheritParams teal_modules+ |
+ ||
| 14 | ++ |
+ #' @param server_args (named `list`)+ |
+ ||
| 15 | ++ |
+ #' Arguments passed to [teal.reporter::reporter_previewer_srv()]. |
||
| 50 | +16 |
- #' as needed. Thus, we do not export this method.+ #' |
||
| 51 | +17 |
- #'+ #' @return |
||
| 52 | +18 |
- #' @param files (`character`) vector of filenames.+ #' `teal_module` (extended with `teal_module_previewer` class) containing the `teal.reporter` previewer functionality. |
||
| 53 | +19 |
#' |
||
| 54 | +20 |
- #' @return `NULL`, invisibly.+ #' @export |
||
| 55 | +21 |
- #' @keywords internal+ #' |
||
| 56 | +22 |
- run_js_files <- function(files) {
+ reporter_previewer_module <- function(label = "Report previewer", server_args = list()) {
|
||
| 57 | -88x | +23 | +7x |
- checkmate::assert_character(files, min.len = 1, any.missing = FALSE)+ checkmate::assert_string(label) |
| 58 | -88x | +24 | +5x |
- lapply(files, function(file) {
+ checkmate::assert_list(server_args, names = "named") |
| 59 | -88x | +25 | +5x |
- shinyjs::runjs(paste0(readLines(system.file("js", file, package = "teal", mustWork = TRUE)), collapse = "\n"))
+ checkmate::assert_true(all(names(server_args) %in% names(formals(teal.reporter::reporter_previewer_srv)))) |
| 60 | +26 |
- })+ |
||
| 61 | -88x | +27 | +3x |
- invisible(NULL)+ message("Initializing reporter_previewer_module")
|
| 62 | +28 |
- }+ |
||
| 63 | -+ | |||
| 29 | +3x |
-
+ srv <- function(id, reporter, ...) {
|
||
| 64 | -+ | |||
| 30 | +! |
- #' Code to include `teal` `CSS` and `JavaScript` files+ teal.reporter::reporter_previewer_srv(id, reporter, ...) |
||
| 65 | +31 |
- #'+ } |
||
| 66 | +32 |
- #' This is useful when you want to use the same `JavaScript` and `CSS` files that are+ |
||
| 67 | -+ | |||
| 33 | +3x |
- #' used with the `teal` application.+ ui <- function(id, ...) {
|
||
| 68 | -+ | |||
| 34 | +! |
- #' This is also useful for running standalone modules in `teal` with the correct+ teal.reporter::reporter_previewer_ui(id, ...) |
||
| 69 | +35 |
- #' styles.+ } |
||
| 70 | +36 |
- #' Also initializes `shinyjs` so you can use it.+ |
||
| 71 | -+ | |||
| 37 | +3x |
- #'+ module <- module( |
||
| 72 | -+ | |||
| 38 | +3x |
- #' Simply add `include_teal_css_js()` as one of the UI elements.+ label = "temporary label", |
||
| 73 | -+ | |||
| 39 | +3x |
- #' @return A `shiny.tag.list`.+ server = srv, ui = ui, |
||
| 74 | -+ | |||
| 40 | +3x |
- #' @keywords internal+ server_args = server_args, ui_args = list(), datanames = NULL |
||
| 75 | +41 |
- include_teal_css_js <- function() {
- |
- ||
| 76 | -! | -
- tagList(+ ) |
||
| 77 | -! | +|||
| 42 | +
- shinyjs::useShinyjs(),+ # Module is created with a placeholder label and the label is changed later. |
|||
| 78 | -! | +|||
| 43 | +
- include_css_files(),+ # This is to prevent another module being labeled "Report previewer". |
|||
| 79 | -+ | |||
| 44 | +3x |
- # init.js is executed from the server+ class(module) <- c(class(module), "teal_module_previewer") |
||
| 80 | -! | +|||
| 45 | +3x |
- include_js_files(except = "init.js"),+ module$label <- label |
||
| 81 | -! | +|||
| 46 | +3x |
- shinyjs::hidden(icon("fas fa-gear")), # add hidden icon to load font-awesome css for icons
+ attr(module, "teal_bookmarkable") <- TRUE |
||
| 82 | -+ | |||
| 47 | +3x |
- )+ module |
||
| 83 | +48 |
}@@ -49241,28 +49241,28 @@ teal coverage - 60.11% |
| 1 |
- #' Show `R` code modal+ setOldClass("teal_data_module")
|
||
| 2 |
- #'+ |
||
| 3 |
- #' @description `r lifecycle::badge("deprecated")`
+ #' Evaluate code on `teal_data_module` |
||
| 5 |
- #' Use the [shiny::showModal()] function to show the `R` code inside.+ #' @details |
||
| 6 |
- #'+ #' `eval_code` evaluates given code in the environment of the `teal_data` object created by the `teal_data_module`. |
||
| 7 |
- #' @param title (`character(1)`)+ #' The code is added to the `@code` slot of the `teal_data`. |
||
| 8 |
- #' Title of the modal, displayed in the first comment of the `R` code.+ #' |
||
| 9 |
- #' @param rcode (`character`)+ #' @param object (`teal_data_module`) |
||
| 10 |
- #' vector with `R` code to show inside the modal.+ #' @inheritParams teal.code::eval_code |
||
| 11 |
- #' @param session (`ShinySession`) optional+ #' |
||
| 12 |
- #' `shiny` session object, defaults to [shiny::getDefaultReactiveDomain()].+ #' @return |
||
| 13 |
- #'+ #' `eval_code` returns a `teal_data_module` object with a delayed evaluation of `code` when the module is run. |
||
| 14 |
- #' @references [shiny::showModal()]+ #' |
||
| 15 |
- #' @export+ #' @examples |
||
| 16 |
- show_rcode_modal <- function(title = NULL, rcode, session = getDefaultReactiveDomain()) {
+ #' eval_code(tdm, "dataset1 <- subset(dataset1, Species == 'virginica')") |
||
| 17 | -! | +
- lifecycle::deprecate_soft(+ #' |
|
| 18 | -! | +
- when = "0.16",+ #' @include teal_data_module.R |
|
| 19 | -! | +
- what = "show_rcode_modal()",+ #' @name eval_code |
|
| 20 | -! | +
- details = "This function will be removed in the next release."+ #' @rdname teal_data_module |
|
| 21 |
- )+ #' @aliases eval_code,teal_data_module,character-method |
||
| 22 |
-
+ #' @aliases eval_code,teal_data_module,language-method |
||
| 23 | -! | +
- rcode <- paste(rcode, collapse = "\n")+ #' @aliases eval_code,teal_data_module,expression-method |
|
| 24 |
-
+ #' |
||
| 25 | -! | +
- ns <- session$ns+ #' @importFrom methods setMethod |
|
| 26 | -! | +
- showModal(modalDialog(+ #' @importMethodsFrom teal.code eval_code |
|
| 27 | -! | +
- tagList(+ #' |
|
| 28 | -! | +
- tags$div(+ setMethod("eval_code", signature = c("teal_data_module", "character"), function(object, code) {
|
|
| 29 | -! | +9x |
- actionButton(ns("copyRCode"), "Copy to Clipboard", `data-clipboard-target` = paste0("#", ns("r_code"))),
+ teal_data_module( |
| 30 | -! | +9x |
- modalButton("Dismiss"),
+ ui = function(id) {
|
| 31 | -! | +1x |
- style = "mb-4"+ ns <- NS(id) |
| 32 | -+ | 1x |
- ),+ object$ui(ns("mutate_inner"))
|
| 33 | -! | +
- tags$div(tags$pre(id = ns("r_code"), rcode)),
+ }, |
|
| 34 | -+ | 9x |
- ),+ server = function(id) {
|
| 35 | -! | +7x |
- title = title,+ moduleServer(id, function(input, output, session) {
|
| 36 | -! | +7x |
- footer = tagList(+ data <- object$server("mutate_inner")
|
| 37 | -! | +6x |
- actionButton(ns("copyRCode"), "Copy to Clipboard", `data-clipboard-target` = paste0("#", ns("r_code"))),
+ td <- eventReactive(data(), |
| 38 | -! | +
- modalButton("Dismiss")
+ {
|
|
| 39 | -+ | 6x |
- ),+ if (inherits(data(), c("teal_data", "qenv.error"))) {
|
| 40 | -! | +4x |
- size = "l",+ eval_code(data(), code) |
| 41 | -! | +
- easyClose = TRUE+ } else {
|
|
| 42 | -+ | 2x |
- ))+ data() |
| 43 |
- }+ }+ |
+ ||
| 44 | ++ |
+ },+ |
+ |
| 45 | +6x | +
+ ignoreNULL = FALSE+ |
+ |
| 46 | ++ |
+ )+ |
+ |
| 47 | +6x | +
+ td+ |
+ |
| 48 | ++ |
+ })+ |
+ |
| 49 | ++ |
+ }+ |
+ |
| 50 | ++ |
+ )+ |
+ |
| 51 | ++ |
+ })+ |
+ |
| 52 | ++ | + + | +|
| 53 | ++ |
+ setMethod("eval_code", signature = c("teal_data_module", "language"), function(object, code) {
+ |
+ |
| 54 | +1x | +
+ eval_code(object, code = paste(lang2calls(code), collapse = "\n"))+ |
+ |
| 55 | ++ |
+ })+ |
+ |
| 56 | ++ | + + | +|
| 57 | ++ |
+ setMethod("eval_code", signature = c("teal_data_module", "expression"), function(object, code) {
+ |
+ |
| 58 | +2x | +
+ eval_code(object, code = paste(lang2calls(code), collapse = "\n"))+ |
+ |
| 59 | ++ |
+ }) |
| 1 |
- setOldClass("teal_data_module")
+ #' Store and restore `teal_slices` object |
|||
| 2 |
-
+ #' |
|||
| 3 |
- #' Evaluate code on `teal_data_module`+ #' Functions that write a `teal_slices` object to a file in the `JSON` format, |
|||
| 4 |
- #'+ #' and also restore the object from disk. |
|||
| 5 |
- #' @details+ #' |
|||
| 6 |
- #' `eval_code` evaluates given code in the environment of the `teal_data` object created by the `teal_data_module`.+ #' Date and date time objects are stored in the following formats: |
|||
| 7 |
- #' The code is added to the `@code` slot of the `teal_data`.+ #' |
|||
| 8 |
- #'+ #' - `Date` class is converted to the `"ISO8601"` standard (`YYYY-MM-DD`). |
|||
| 9 |
- #' @param object (`teal_data_module`)+ #' - `POSIX*t` classes are converted to character by using |
|||
| 10 |
- #' @inheritParams teal.code::eval_code+ #' `format.POSIX*t(usetz = TRUE, tz = "UTC")` (`YYYY-MM-DD HH:MM:SS UTC`, where |
|||
| 11 |
- #'+ #' `UTC` is the `Coordinated Universal Time` timezone short-code). |
|||
| 12 |
- #' @return+ #' |
|||
| 13 |
- #' `eval_code` returns a `teal_data_module` object with a delayed evaluation of `code` when the module is run.+ #' This format is assumed during `slices_restore`. All `POSIX*t` objects in |
|||
| 14 |
- #'+ #' `selected` or `choices` fields of `teal_slice` objects are always printed in |
|||
| 15 |
- #' @examples+ #' `UTC` timezone as well. |
|||
| 16 |
- #' eval_code(tdm, "dataset1 <- subset(dataset1, Species == 'virginica')")+ #' |
|||
| 17 |
- #'+ #' @param tss (`teal_slices`) object to be stored. |
|||
| 18 |
- #' @include teal_data_module.R+ #' @param file (`character(1)`) file path where `teal_slices` object will be |
|||
| 19 |
- #' @name eval_code+ #' saved and restored. The file extension should be `".json"`. |
|||
| 20 |
- #' @rdname teal_data_module+ #' |
|||
| 21 |
- #' @aliases eval_code,teal_data_module,character-method+ #' @return `slices_store` returns `NULL`, invisibly. |
|||
| 22 |
- #' @aliases eval_code,teal_data_module,language-method+ #' |
|||
| 23 |
- #' @aliases eval_code,teal_data_module,expression-method+ #' @seealso [teal_slices()] |
|||
| 25 |
- #' @importFrom methods setMethod+ #' @keywords internal |
|||
| 26 |
- #' @importMethodsFrom teal.code eval_code+ #' |
|||
| 27 |
- #'+ slices_store <- function(tss, file) {
|
|||
| 28 | -+ | 9x |
- setMethod("eval_code", signature = c("teal_data_module", "character"), function(object, code) {
+ checkmate::assert_class(tss, "teal_slices") |
|
| 29 | 9x |
- teal_data_module(+ checkmate::assert_path_for_output(file, overwrite = TRUE, extension = "json") |
||
| 30 | -9x | +
- ui = function(id) {
+
|
||
| 31 | -1x | +9x |
- ns <- NS(id)+ cat(format(tss, trim_lines = FALSE), "\n", file = file) |
|
| 32 | -1x | +
- object$ui(ns("mutate_inner"))
+ } |
||
| 33 |
- },+ |
|||
| 34 | -9x | +
- server = function(id) {
+ #' @rdname slices_store |
||
| 35 | -7x | +
- moduleServer(id, function(input, output, session) {
+ #' @return `slices_restore` returns a `teal_slices` object restored from the file. |
||
| 36 | -7x | +
- teal_data_rv <- object$server("mutate_inner")
+ #' @keywords internal |
||
| 37 | -6x | +
- td <- eventReactive(teal_data_rv(),+ slices_restore <- function(file) {
|
||
| 38 | -+ | 9x |
- {
+ checkmate::assert_file_exists(file, access = "r", extension = "json") |
|
| 39 | -6x | +
- if (inherits(teal_data_rv(), c("teal_data", "qenv.error"))) {
+
|
||
| 40 | -4x | +9x |
- eval_code(teal_data_rv(), code)+ tss_json <- jsonlite::fromJSON(file, simplifyDataFrame = FALSE) |
|
| 41 | -+ | 9x |
- } else {
+ tss_json$slices <- |
|
| 42 | -2x | +9x |
- teal_data_rv()+ lapply(tss_json$slices, function(slice) {
|
|
| 43 | -+ | 9x |
- }+ for (field in c("selected", "choices")) {
|
|
| 44 | -+ | 18x |
- },+ if (!is.null(slice[[field]])) {
|
|
| 45 | -6x | +12x |
- ignoreNULL = FALSE+ if (length(slice[[field]]) > 0) {
|
|
| 46 | -+ | 9x |
- )+ date_partial_regex <- "^[0-9]{4}-[0-9]{2}-[0-9]{2}"
|
|
| 47 | -6x | +9x |
- td+ time_stamp_regex <- paste0(date_partial_regex, "\\s[0-9]{2}:[0-9]{2}:[0-9]{2}\\sUTC$")
|
|
| 48 |
- })+ |
|||
| 49 | +9x | +
+ slice[[field]] <-+ |
+ ||
| 50 | +9x | +
+ if (all(grepl(paste0(date_partial_regex, "$"), slice[[field]]))) {
+ |
+ ||
| 51 | +3x | +
+ as.Date(slice[[field]])+ |
+ ||
| 52 | +9x | +
+ } else if (all(grepl(time_stamp_regex, slice[[field]]))) {
+ |
+ ||
| 53 | +3x | +
+ as.POSIXct(slice[[field]], tz = "UTC")+ |
+ ||
| 54 |
- }+ } else {
+ |
+ |||
| 55 | +3x | +
+ slice[[field]] |
||
| 50 | +56 |
- )+ } |
||
| 51 | +57 |
- })+ } else {
+ |
+ ||
| 58 | +3x | +
+ slice[[field]] <- character(0) |
||
| 52 | +59 |
-
+ } |
||
| 53 | +60 |
- setMethod("eval_code", signature = c("teal_data_module", "language"), function(object, code) {
+ }+ |
+ ||
| 61 | ++ |
+ } |
||
| 54 | -1x | +62 | +9x |
- eval_code(object, code = paste(lang2calls(code), collapse = "\n"))+ slice |
| 55 | +63 |
- })+ }) |
||
| 56 | +64 | |||
| 65 | +9x | +
+ tss_elements <- lapply(tss_json$slices, as.teal_slice)+ |
+ ||
| 57 | +66 |
- setMethod("eval_code", signature = c("teal_data_module", "expression"), function(object, code) {
+
|
||
| 58 | -2x | +67 | +9x |
- eval_code(object, code = paste(lang2calls(code), collapse = "\n"))+ do.call(teal_slices, c(tss_elements, tss_json$attributes)) |
| 59 | +68 |
- })+ } |
| 1 |
- #' Create a `tdata` object+ #' Show `R` code modal |
||
| 3 |
- #' @description `r lifecycle::badge("superseded")`
+ #' @description `r lifecycle::badge("deprecated")`
|
||
| 5 |
- #' Recent changes in `teal` cause modules to fail because modules expect a `tdata` object+ #' Use the [shiny::showModal()] function to show the `R` code inside. |
||
| 6 |
- #' to be passed to the `data` argument but instead they receive a `teal_data` object,+ #' |
||
| 7 |
- #' which is additionally wrapped in a reactive expression in the server functions.+ #' @param title (`character(1)`) |
||
| 8 |
- #' In order to easily adapt such modules without a proper refactor,+ #' Title of the modal, displayed in the first comment of the `R` code. |
||
| 9 |
- #' use this function to downgrade the `data` argument.+ #' @param rcode (`character`) |
||
| 10 |
- #'+ #' vector with `R` code to show inside the modal. |
||
| 11 |
- #' @name tdata+ #' @param session (`ShinySession`) optional |
||
| 12 |
- #' @param ... ignored+ #' `shiny` session object, defaults to [shiny::getDefaultReactiveDomain()]. |
||
| 13 |
- #' @return nothing+ #' |
||
| 14 |
- NULL+ #' @references [shiny::showModal()] |
||
| 15 |
-
+ #' @export |
||
| 16 |
- #' @rdname tdata+ show_rcode_modal <- function(title = NULL, rcode, session = getDefaultReactiveDomain()) {
|
||
| 17 | -+ | ! |
- #' @export+ lifecycle::deprecate_soft( |
| 18 | -+ | ! |
- new_tdata <- function(...) {
+ when = "0.16", |
| 19 | ! |
- .deprecate_tdata_msg()+ what = "show_rcode_modal()", |
|
| 20 | -+ | ! |
- }+ details = "This function will be removed in the next release." |
| 21 |
-
+ ) |
||
| 22 |
- #' @rdname tdata+ |
||
| 23 | -+ | ! |
- #' @export+ rcode <- paste(rcode, collapse = "\n") |
| 24 |
- tdata2env <- function(...) {
+
|
||
| 25 | ! |
- .deprecate_tdata_msg()+ ns <- session$ns |
|
| 26 | -+ | ! |
- }+ showModal(modalDialog( |
| 27 | -+ | ! |
-
+ tagList( |
| 28 | -+ | ! |
- #' @rdname tdata+ tags$div( |
| 29 | -+ | ! |
- #' @export+ actionButton(ns("copyRCode"), "Copy to Clipboard", `data-clipboard-target` = paste0("#", ns("r_code"))),
|
| 30 | -+ | ! |
- get_code_tdata <- function(...) {
+ modalButton("Dismiss"),
|
| 31 | ! |
- .deprecate_tdata_msg()+ style = "mb-4" |
|
| 32 |
- }+ ), |
||
| 33 | -+ | ! |
-
+ tags$div(tags$pre(id = ns("r_code"), rcode)),
|
| 34 |
- #' @rdname tdata+ ), |
||
| 35 | -- |
- #' @export- |
- |
| 36 | -+ | ! |
- join_keys.tdata <- function(...) {
+ title = title, |
| 37 | +36 | ! |
- .deprecate_tdata_msg()- |
-
| 38 | -- |
- }- |
- |
| 39 | -- | - - | -|
| 40 | -- |
- #' @rdname tdata- |
- |
| 41 | -- |
- #' @export- |
- |
| 42 | -- |
- get_metadata <- function(...) {
+ footer = tagList( |
|
| 43 | +37 | ! |
- .deprecate_tdata_msg()- |
-
| 44 | -- |
- }- |
- |
| 45 | -- | - - | -|
| 46 | -- |
- #' @rdname tdata- |
- |
| 47 | -- |
- #' @export- |
- |
| 48 | -- |
- as_tdata <- function(...) {
+ actionButton(ns("copyRCode"), "Copy to Clipboard", `data-clipboard-target` = paste0("#", ns("r_code"))),
|
|
| 49 | +38 | ! |
- .deprecate_tdata_msg()- |
-
| 50 | -- |
- }- |
- |
| 51 | -- | - - | -|
| 52 | -- |
-
+ modalButton("Dismiss")
|
|
| 53 | +39 |
- .deprecate_tdata_msg <- function() {
- |
- |
| 54 | -! | -
- lifecycle::deprecate_stop(- |
- |
| 55 | -! | -
- when = "0.16",- |
- |
| 56 | -! | -
- what = "tdata()",- |
- |
| 57 | -! | -
- details = paste(+ ), |
|
| 58 | +40 | ! |
- "tdata has been removed in favour of `teal_data`.\n",+ size = "l", |
| 59 | +41 | ! |
- "Please follow migration instructions https://github.com/insightsengineering/teal/discussions/987."- |
-
| 60 | -- |
- )+ easyClose = TRUE |
|
| 61 | +42 |
- )+ )) |
|
| 62 | +43 |
} |