| 1 |
- # FilteredData ------+ #' Create a `teal` module for previewing a report |
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| 2 |
-
+ #' |
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| 3 |
- #' Drive a `teal` application+ #' @description `r lifecycle::badge("experimental")`
|
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| 5 |
- #' Extension of the `shinytest2::AppDriver` class with methods for+ #' This function wraps [teal.reporter::reporter_previewer_ui()] and |
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| 6 |
- #' driving a teal application for performing interactions for `shinytest2` tests.+ #' [teal.reporter::reporter_previewer_srv()] into a `teal_module` to be |
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| 7 |
- #'+ #' used in `teal` applications. |
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| 8 |
- #' @keywords internal+ #' |
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| 9 |
- #'+ #' If you are creating a `teal` application using [init()] then this |
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| 10 |
- TealAppDriver <- R6::R6Class( # nolint: object_name.+ #' module will be added to your application automatically if any of your `teal_modules` |
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| 11 |
- "TealAppDriver",+ #' support report generation. |
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| 12 |
- inherit = {
+ #' |
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| 13 |
- if (!requireNamespace("shinytest2", quietly = TRUE)) {
+ #' @inheritParams teal_modules |
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| 14 |
- stop("Please install 'shinytest2' package to use this class.")
+ #' @param server_args (named `list`) |
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| 15 |
- }+ #' Arguments passed to [teal.reporter::reporter_previewer_srv()]. |
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| 16 |
- if (!requireNamespace("rvest", quietly = TRUE)) {
+ #' |
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| 17 |
- stop("Please install 'rvest' package to use this class.")
+ #' @return |
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| 18 |
- }+ #' `teal_module` (extended with `teal_module_previewer` class) containing the `teal.reporter` previewer functionality. |
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| 19 |
- shinytest2::AppDriver+ #' |
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| 20 |
- },+ #' @export |
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| 21 |
- # public methods ----+ #' |
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| 22 |
- public = list(+ reporter_previewer_module <- function(label = "Report previewer", server_args = list()) {
|
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| 23 | -+ | 7x |
- #' @description+ checkmate::assert_string(label) |
| 24 | -+ | 5x |
- #' Initialize a `TealAppDriver` object for testing a `teal` application.+ 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 |
- #' @param data,modules,filter,title,header,footer,landing_popup arguments passed to `init`+ |
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| 27 | -+ | 3x |
- #' @param timeout (`numeric`) Default number of milliseconds for any timeout or+ message("Initializing reporter_previewer_module")
|
| 28 |
- #' timeout_ parameter in the `TealAppDriver` class.+ |
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| 29 | -+ | 3x |
- #' Defaults to 20s.+ srv <- function(id, reporter, ...) {
|
| 30 | -+ | ! |
- #'+ teal.reporter::reporter_previewer_srv(id, reporter, ...) |
| 31 |
- #' See [`shinytest2::AppDriver`] `new` method for more details on how to change it+ } |
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| 32 |
- #' via options or environment variables.+ |
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| 33 | -+ | 3x |
- #' @param load_timeout (`numeric`) How long to wait for the app to load, in ms.+ ui <- function(id, ...) {
|
| 34 | -+ | ! |
- #' This includes the time to start R. Defaults to 100s.+ teal.reporter::reporter_previewer_ui(id, ...) |
| 35 |
- #'+ } |
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| 36 |
- #' See [`shinytest2::AppDriver`] `new` method for more details on how to change it+ |
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| 37 | -+ | 3x |
- #' via options or environment variables+ module <- module( |
| 38 | -+ | 3x |
- #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$new`+ label = "temporary label", |
| 39 | -+ | 3x |
- #'+ server = srv, ui = ui, |
| 40 | -+ | 3x |
- #'+ server_args = server_args, ui_args = list(), datanames = NULL |
| 41 |
- #' @return Object of class `TealAppDriver`+ ) |
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| 42 |
- initialize = function(data,+ # Module is created with a placeholder label and the label is changed later. |
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| 43 |
- modules,+ # This is to prevent another module being labeled "Report previewer". |
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| 44 | -+ | 3x |
- filter = teal_slices(),+ class(module) <- c(class(module), "teal_module_previewer") |
| 45 | -+ | 3x |
- title = build_app_title(),+ module$label <- label |
| 46 | -+ | 3x |
- header = tags$p(),+ attr(module, "teal_bookmarkable") <- TRUE |
| 47 | -+ | 3x |
- footer = tags$p(),+ module |
| 48 |
- landing_popup = NULL,+ } |
| 49 | +1 |
- timeout = rlang::missing_arg(),+ #' Get client timezone |
|
| 50 | +2 |
- load_timeout = rlang::missing_arg(),+ #' |
|
| 51 | +3 |
- ...) {
- |
- |
| 52 | -! | -
- private$data <- data- |
- |
| 53 | -! | -
- private$modules <- modules- |
- |
| 54 | -! | -
- private$filter <- filter- |
- |
| 55 | -! | -
- app <- init(- |
- |
| 56 | -! | -
- data = data,- |
- |
| 57 | -! | -
- modules = modules,+ #' User timezone in the browser may be different to the one on the server. |
|
| 58 | -! | +||
| 4 | +
- filter = filter,+ #' This script can be run to register a `shiny` input which contains information about the timezone in the browser. |
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| 59 | -! | +||
| 5 | +
- title = title,+ #' |
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| 60 | -! | +||
| 6 | +
- header = header,+ #' @param ns (`function`) namespace function passed from the `session` object in the `shiny` server. |
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| 61 | -! | +||
| 7 | +
- footer = footer,+ #' For `shiny` modules this will allow for proper name spacing of the registered input. |
||
| 62 | -! | +||
| 8 | +
- landing_popup = landing_popup,+ #' |
||
| 63 | +9 |
- )+ #' @return `NULL`, invisibly. |
|
| 64 | +10 |
-
+ #' |
|
| 65 | +11 |
- # Default timeout is hardcoded to 4s in shinytest2:::resolve_timeout+ #' @keywords internal |
|
| 66 | +12 |
- # It must be set as parameter to the AppDriver+ #' |
|
| 67 | -! | +||
| 13 | +
- suppressWarnings(+ get_client_timezone <- function(ns) {
|
||
| 68 | -! | +||
| 14 | +81x |
- super$initialize(+ script <- sprintf( |
|
| 69 | -! | +||
| 15 | +81x |
- app_dir = shinyApp(app$ui, app$server),+ "Shiny.setInputValue(`%s`, Intl.DateTimeFormat().resolvedOptions().timeZone)", |
|
| 70 | -! | +||
| 16 | +81x |
- name = "teal",+ ns("timezone")
|
|
| 71 | -! | +||
| 17 | +
- variant = shinytest2::platform_variant(),+ ) |
||
| 72 | -! | +||
| 18 | +81x |
- timeout = rlang::maybe_missing(timeout, 20 * 1000),+ shinyjs::runjs(script) # function does not return anything |
|
| 73 | -! | +||
| 19 | +81x |
- load_timeout = rlang::maybe_missing(load_timeout, 100 * 1000),+ invisible(NULL) |
|
| 74 | +20 |
- ...+ } |
|
| 75 | +21 |
- )+ |
|
| 76 | +22 |
- )+ #' Resolve the expected bootstrap theme |
|
| 77 | +23 |
-
+ #' @noRd |
|
| 78 | +24 |
- # Check for minimum version of Chrome that supports the tests+ #' @keywords internal |
|
| 79 | +25 |
- # - Element.checkVisibility was added on 105- |
- |
| 80 | -! | -
- chrome_version <- numeric_version(- |
- |
| 81 | -! | -
- gsub(+ get_teal_bs_theme <- function() {
|
|
| 82 | -! | +||
| 26 | +4x |
- "[[:alnum:]_]+/", # Prefix that ends with forward slash+ bs_theme <- getOption("teal.bs_theme")
|
|
| 83 | +27 |
- "",- |
- |
| 84 | -! | -
- self$get_chromote_session()$Browser$getVersion()$product+ |
|
| 85 | -+ | ||
| 28 | +4x |
- ),+ if (is.null(bs_theme)) {
|
|
| 86 | -! | +||
| 29 | +1x |
- strict = FALSE+ return(NULL) |
|
| 87 | +30 |
- )+ } |
|
| 88 | +31 | ||
| 89 | -! | +||
| 32 | +3x |
- required_version <- "121"+ if (!checkmate::test_class(bs_theme, "bs_theme")) {
|
|
| 90 | -+ | ||
| 33 | +2x |
-
+ warning( |
|
| 91 | -! | +||
| 34 | +2x |
- testthat::skip_if(+ "Assertion on 'teal.bs_theme' option value failed: ", |
|
| 92 | -! | +||
| 35 | +2x |
- is.na(chrome_version),+ checkmate::check_class(bs_theme, "bs_theme"), |
|
| 93 | -! | +||
| 36 | +2x |
- "Problem getting Chrome version, please contact the developers."+ ". The default Shiny Bootstrap theme will be used." |
|
| 94 | +37 |
- )+ ) |
|
| 95 | -! | +||
| 38 | +2x |
- testthat::skip_if(+ return(NULL) |
|
| 96 | -! | +||
| 39 | +
- chrome_version < required_version,+ } |
||
| 97 | -! | +||
| 40 | +
- sprintf(+ |
||
| 98 | -! | +||
| 41 | +1x |
- "Chrome version '%s' is not supported, please upgrade to '%s' or higher",+ bs_theme |
|
| 99 | -! | +||
| 42 | +
- chrome_version,+ } |
||
| 100 | -! | +||
| 43 | +
- required_version+ |
||
| 101 | +44 |
- )+ #' Return parentnames along with datanames. |
|
| 102 | +45 |
- )+ #' @noRd |
|
| 103 | +46 |
- # end od check+ #' @keywords internal |
|
| 104 | +47 |
-
+ .include_parent_datanames <- function(datanames, join_keys) {
|
|
| 105 | -! | +||
| 48 | +163x |
- private$set_active_ns()+ ordered_datanames <- datanames |
|
| 106 | -! | +||
| 49 | +163x |
- self$wait_for_idle()+ for (i in datanames) {
|
|
| 107 | -+ | ||
| 50 | +293x |
- },+ parents <- character(0) |
|
| 108 | -+ | ||
| 51 | +293x |
- #' @description+ while (length(i) > 0) {
|
|
| 109 | -+ | ||
| 52 | +306x |
- #' Append parent [`shinytest2::AppDriver`] `click` method with a call to `waif_for_idle()` method.+ parent_i <- teal.data::parent(join_keys, i) |
|
| 110 | -+ | ||
| 53 | +306x |
- #' @param ... arguments passed to parent [`shinytest2::AppDriver`] `click()` method.+ parents <- c(parent_i, parents) |
|
| 111 | -+ | ||
| 54 | +306x |
- click = function(...) {
+ i <- parent_i |
|
| 112 | -! | +||
| 55 | +
- super$click(...)+ } |
||
| 113 | -! | +||
| 56 | +293x |
- private$wait_for_page_stability()+ ordered_datanames <- c(parents, ordered_datanames) |
|
| 114 | +57 |
- },+ } |
|
| 115 | -+ | ||
| 58 | +163x |
- #' @description+ unique(ordered_datanames) |
|
| 116 | +59 |
- #' Check if the app has shiny errors. This checks for global shiny errors.+ } |
|
| 117 | +60 |
- #' Note that any shiny errors dependent on shiny server render will only be captured after the teal module tab+ |
|
| 118 | +61 |
- #' is visited because shiny will not trigger server computations when the tab is invisible.+ #' Return topologicaly sorted datanames |
|
| 119 | +62 |
- #' So, navigate to the module tab you want to test before calling this function.+ #' @noRd |
|
| 120 | +63 |
- #' Although, this catches errors hidden in the other module tabs if they are already rendered.+ #' @keywords internal |
|
| 121 | +64 |
- expect_no_shiny_error = function() {
+ .topologically_sort_datanames <- function(datanames, join_keys) {
|
|
| 122 | -! | +||
| 65 | +131x |
- testthat::expect_null(+ datanames_with_parents <- .include_parent_datanames(datanames, join_keys) |
|
| 123 | -! | +||
| 66 | +131x |
- self$get_html(".shiny-output-error:not(.shiny-output-error-validation)"),
+ intersect(datanames, datanames_with_parents) |
|
| 124 | -! | +||
| 67 | +
- info = "Shiny error is observed"+ } |
||
| 125 | +68 |
- )+ |
|
| 126 | +69 |
- },+ #' Create a `FilteredData` |
|
| 127 | +70 |
- #' @description+ #' |
|
| 128 | +71 |
- #' Check if the app has no validation errors. This checks for global shiny validation errors.+ #' Create a `FilteredData` object from a `teal_data` object. |
|
| 129 | +72 |
- expect_no_validation_error = function() {
+ #' |
|
| 130 | -! | +||
| 73 | +
- testthat::expect_null(+ #' @param x (`teal_data`) object |
||
| 131 | -! | +||
| 74 | +
- self$get_html(".shiny-output-error-validation"),
+ #' @param datanames (`character`) vector of data set names to include; must be subset of `datanames(x)` |
||
| 132 | -! | +||
| 75 | +
- info = "No validation error is observed"+ #' @return A `FilteredData` object. |
||
| 133 | +76 |
- )+ #' @keywords internal |
|
| 134 | +77 |
- },+ teal_data_to_filtered_data <- function(x, datanames = ls(teal.code::get_env(x))) {
|
|
| 135 | -+ | ||
| 78 | +76x |
- #' @description+ checkmate::assert_class(x, "teal_data") |
|
| 136 | -+ | ||
| 79 | +76x |
- #' Check if the app has validation errors. This checks for global shiny validation errors.+ checkmate::assert_character(datanames, min.chars = 1L, any.missing = FALSE) |
|
| 137 | +80 |
- expect_validation_error = function() {
+ # Otherwise, FilteredData will be created in the modules' scope later |
|
| 138 | -! | +||
| 81 | +76x |
- testthat::expect_false(+ teal.slice::init_filtered_data( |
|
| 139 | -! | +||
| 82 | +76x |
- is.null(self$get_html(".shiny-output-error-validation")),
+ x = Filter( |
|
| 140 | -! | +||
| 83 | +76x |
- info = "Validation error is not observed"+ length, |
|
| 141 | -+ | ||
| 84 | +76x |
- )+ sapply(datanames, function(dn) x[[dn]], simplify = FALSE) |
|
| 142 | +85 |
- },+ ), |
|
| 143 | -+ | ||
| 86 | +76x |
- #' @description+ join_keys = teal.data::join_keys(x) |
|
| 144 | +87 |
- #' Set the input in the `teal` app.+ ) |
|
| 145 | +88 |
- #'+ } |
|
| 146 | +89 |
- #' @param input_id (character) The shiny input id with it's complete name space.+ |
|
| 147 | +90 |
- #' @param value The value to set the input to.+ |
|
| 148 | +91 |
- #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$set_inputs`+ #' Template function for `TealReportCard` creation and customization |
|
| 149 | +92 |
- #'+ #' |
|
| 150 | +93 |
- #' @return The `TealAppDriver` object invisibly.+ #' This function generates a report card with a title, |
|
| 151 | +94 |
- set_input = function(input_id, value, ...) {
- |
- |
| 152 | -! | -
- do.call(- |
- |
| 153 | -! | -
- self$set_inputs,+ #' an optional description, and the option to append the filter state list. |
|
| 154 | -! | +||
| 95 | +
- c(setNames(list(value), input_id), list(...))+ #' |
||
| 155 | +96 |
- )+ #' @param title (`character(1)`) title of the card (unless overwritten by label) |
|
| 156 | -! | +||
| 97 | +
- invisible(self)+ #' @param label (`character(1)`) label provided by the user when adding the card |
||
| 157 | +98 |
- },+ #' @param description (`character(1)`) optional, additional description |
|
| 158 | +99 |
- #' @description+ #' @param with_filter (`logical(1)`) flag indicating to add filter state |
|
| 159 | +100 |
- #' Navigate the teal tabs in the `teal` app.+ #' @param filter_panel_api (`FilterPanelAPI`) object with API that allows the generation |
|
| 160 | +101 |
- #'+ #' of the filter state in the report |
|
| 161 | +102 |
- #' @param tabs (character) Labels of tabs to navigate to. The order of the tabs is important,+ #' |
|
| 162 | +103 |
- #' and it should start with the most parent level tab.+ #' @return (`TealReportCard`) populated with a title, description and filter state. |
|
| 163 | +104 |
- #' Note: In case the teal tab group has duplicate names, the first tab will be selected,+ #' |
|
| 164 | +105 |
- #' If you wish to select the second tab with the same name, use the suffix "_1".+ #' @export |
|
| 165 | +106 |
- #' If you wish to select the third tab with the same name, use the suffix "_2" and so on.+ report_card_template <- function(title, label, description = NULL, with_filter, filter_panel_api) {
|
|
| 166 | -+ | ||
| 107 | +2x |
- #'+ checkmate::assert_string(title) |
|
| 167 | -+ | ||
| 108 | +2x |
- #' @return The `TealAppDriver` object invisibly.+ checkmate::assert_string(label) |
|
| 168 | -+ | ||
| 109 | +2x |
- navigate_teal_tab = function(tabs) {
+ checkmate::assert_string(description, null.ok = TRUE) |
|
| 169 | -! | +||
| 110 | +2x |
- checkmate::check_character(tabs, min.len = 1)+ checkmate::assert_flag(with_filter) |
|
| 170 | -! | +||
| 111 | +2x |
- for (tab in tabs) {
+ checkmate::assert_class(filter_panel_api, classes = "FilterPanelAPI") |
|
| 171 | -! | +||
| 112 | +
- self$set_input(+ |
||
| 172 | -! | +||
| 113 | +2x |
- "teal-teal_modules-active_tab",+ card <- teal::TealReportCard$new() |
|
| 173 | -! | +||
| 114 | +2x |
- get_unique_labels(tab),+ title <- if (label == "") title else label |
|
| 174 | -! | +||
| 115 | +2x |
- wait_ = FALSE+ card$set_name(title) |
|
| 175 | -+ | ||
| 116 | +2x |
- )+ card$append_text(title, "header2") |
|
| 176 | -+ | ||
| 117 | +1x |
- }+ if (!is.null(description)) card$append_text(description, "header3") |
|
| 177 | -! | +||
| 118 | +1x |
- self$wait_for_idle()+ if (with_filter) card$append_fs(filter_panel_api$get_filter_state()) |
|
| 178 | -! | +||
| 119 | +2x |
- private$set_active_ns()+ card |
|
| 179 | -! | +||
| 120 | +
- invisible(self)+ } |
||
| 180 | +121 |
- },+ |
|
| 181 | +122 |
- #' @description+ |
|
| 182 | +123 |
- #' Get the active shiny name space for different components of the teal app.+ #' Check `datanames` in modules |
|
| 183 | +124 |
- #'+ #' |
|
| 184 | +125 |
- #' @return (`list`) The list of active shiny name space of the teal components.+ #' These functions check if specified `datanames` in modules match those in the data object, |
|
| 185 | +126 |
- active_ns = function() {
+ #' returning error messages or `TRUE` for successful validation. Two functions return error message |
|
| 186 | -! | +||
| 127 | +
- if (identical(private$ns$module, character(0))) {
+ #' in different forms: |
||
| 187 | -! | +||
| 128 | +
- private$set_active_ns()+ #' - `check_modules_datanames` returns `character(1)` for basic assertion usage |
||
| 188 | +129 |
- }+ #' - `check_modules_datanames_html` returns `shiny.tag.list` to display it in the app. |
|
| 189 | -! | +||
| 130 | +
- private$ns+ #' |
||
| 190 | +131 |
- },+ #' @param modules (`teal_modules`) object |
|
| 191 | +132 |
- #' @description+ #' @param datanames (`character`) names of datasets available in the `data` object |
|
| 192 | +133 |
- #' Get the active shiny name space for interacting with the module content.+ #' |
|
| 193 | +134 |
- #'+ #' @return `TRUE` if validation passes, otherwise `character(1)` or `shiny.tag.list` |
|
| 194 | +135 |
- #' @return (`string`) The active shiny name space of the component.+ #' @keywords internal |
|
| 195 | +136 |
- active_module_ns = function() {
+ check_modules_datanames <- function(modules, datanames) {
|
|
| 196 | -! | +||
| 137 | +9x |
- if (identical(private$ns$module, character(0))) {
+ out <- check_modules_datanames_html(modules, datanames) |
|
| 197 | -! | +||
| 138 | +9x |
- private$set_active_ns()+ if (inherits(out, "shiny.tag.list")) {
|
|
| 198 | -+ | ||
| 139 | +3x |
- }+ out_with_ticks <- gsub("<code>|</code>", "`", toString(out))
|
|
| 199 | -! | +||
| 140 | +3x |
- private$ns$module+ out_text <- gsub("<[^<>]+>", "", toString(out_with_ticks))
|
|
| 200 | -+ | ||
| 141 | +3x |
- },+ trimws(gsub("[[:space:]]+", " ", out_text))
|
|
| 201 | +142 |
- #' @description- |
- |
| 202 | -- |
- #' Get the active shiny name space bound with a custom `element` name.- |
- |
| 203 | -- |
- #'+ } else {
|
|
| 204 | -+ | ||
| 143 | +6x |
- #' @param element `character(1)` custom element name.+ out |
|
| 205 | +144 |
- #'+ } |
|
| 206 | +145 |
- #' @return (`string`) The active shiny name space of the component bound with the input `element`.+ } |
|
| 207 | +146 |
- active_module_element = function(element) {
- |
- |
| 208 | -! | -
- checkmate::assert_string(element)- |
- |
| 209 | -! | -
- sprintf("#%s-%s", self$active_module_ns(), element)
+
|
|
| 210 | +147 |
- },+ #' @rdname check_modules_datanames |
|
| 211 | +148 |
- #' @description+ check_modules_datanames_html <- function(modules, |
|
| 212 | +149 |
- #' Get the text of the active shiny name space bound with a custom `element` name.+ datanames) {
|
|
| 213 | -+ | ||
| 150 | +173x |
- #'+ check_datanames <- check_modules_datanames_recursive(modules, datanames) |
|
| 214 | -+ | ||
| 151 | +173x |
- #' @param element `character(1)` the text of the custom element name.+ show_module_info <- inherits(modules, "teal_modules") # used in two contexts - module and app |
|
| 215 | -+ | ||
| 152 | +173x |
- #'+ if (!length(check_datanames)) {
|
|
| 216 | -+ | ||
| 153 | +155x |
- #' @return (`string`) The text of the active shiny name space of the component bound with the input `element`.+ return(TRUE) |
|
| 217 | +154 |
- active_module_element_text = function(element) {
+ } |
|
| 218 | -! | +||
| 155 | +18x |
- checkmate::assert_string(element)+ shiny::tagList( |
|
| 219 | -! | +||
| 156 | +18x |
- self$get_text(self$active_module_element(element))+ lapply( |
|
| 220 | -+ | ||
| 157 | +18x |
- },+ check_datanames, |
|
| 221 | -+ | ||
| 158 | +18x |
- #' @description+ function(mod) {
|
|
| 222 | -+ | ||
| 159 | +18x |
- #' Get the active shiny name space for interacting with the filter panel.+ tagList( |
|
| 223 | -+ | ||
| 160 | +18x |
- #'+ tags$span( |
|
| 224 | -+ | ||
| 161 | +18x |
- #' @return (`string`) The active shiny name space of the component.+ tags$span(if (length(mod$missing_datanames) == 1) "Dataset" else "Datasets"), |
|
| 225 | -+ | ||
| 162 | +18x |
- active_filters_ns = function() {
+ to_html_code_list(mod$missing_datanames), |
|
| 226 | -! | +||
| 163 | +18x |
- if (identical(private$ns$filter_panel, character(0))) {
+ tags$span( |
|
| 227 | -! | +||
| 164 | +18x |
- private$set_active_ns()+ paste0( |
|
| 228 | -+ | ||
| 165 | +18x |
- }+ if (length(mod$missing_datanames) > 1) "are missing" else "is missing", |
|
| 229 | -! | +||
| 166 | +18x |
- private$ns$filter_panel+ if (show_module_info) sprintf(" for module '%s'.", mod$label) else "."
|
|
| 230 | +167 |
- },+ ) |
|
| 231 | +168 |
- #' @description+ ) |
|
| 232 | +169 |
- #' Get the active shiny name space for interacting with the data-summary panel.+ ), |
|
| 233 | -+ | ||
| 170 | +18x |
- #'+ if (length(datanames) >= 1) {
|
|
| 234 | -+ | ||
| 171 | +16x |
- #' @return (`string`) The active shiny name space of the data-summary component.+ tagList( |
|
| 235 | -+ | ||
| 172 | +16x |
- active_data_summary_ns = function() {
+ tags$span(if (length(datanames) == 1) "Dataset" else "Datasets"), |
|
| 236 | -! | +||
| 173 | +16x |
- if (identical(private$ns$data_summary, character(0))) {
+ tags$span("available in data:"),
|
|
| 237 | -! | +||
| 174 | +16x |
- private$set_active_ns()+ tagList( |
|
| 238 | -+ | ||
| 175 | +16x |
- }+ tags$span( |
|
| 239 | -! | +||
| 176 | +16x |
- private$ns$data_summary+ to_html_code_list(datanames), |
|
| 240 | -+ | ||
| 177 | +16x |
- },+ tags$span(".", .noWS = "outside"),
|
|
| 241 | -+ | ||
| 178 | +16x |
- #' @description+ .noWS = c("outside")
|
|
| 242 | +179 |
- #' Get the active shiny name space bound with a custom `element` name.+ ) |
|
| 243 | +180 |
- #'+ ) |
|
| 244 | +181 |
- #' @param element `character(1)` custom element name.+ ) |
|
| 245 | +182 |
- #'+ } else {
|
|
| 246 | -+ | ||
| 183 | +2x |
- #' @return (`string`) The active shiny name space of the component bound with the input `element`.+ tags$span("No datasets are available in data.")
|
|
| 247 | +184 |
- active_data_summary_element = function(element) {
- |
- |
| 248 | -! | -
- checkmate::assert_string(element)+ }, |
|
| 249 | -! | +||
| 185 | +18x |
- sprintf("#%s-%s", self$active_data_summary_ns(), element)
+ tags$br(.noWS = "before") |
|
| 250 | +186 |
- },+ ) |
|
| 251 | +187 |
- #' @description+ } |
|
| 252 | +188 |
- #' Get the input from the module in the `teal` app.+ ) |
|
| 253 | +189 |
- #' This function will only access inputs from the name space of the current active teal module.+ ) |
|
| 254 | +190 |
- #'+ } |
|
| 255 | +191 |
- #' @param input_id (character) The shiny input id to get the value from.+ |
|
| 256 | +192 |
- #'+ #' Recursively checks modules and returns list for every datanames mismatch between module and data |
|
| 257 | +193 |
- #' @return The value of the shiny input.+ #' @noRd |
|
| 258 | +194 |
- get_active_module_input = function(input_id) {
+ check_modules_datanames_recursive <- function(modules, datanames) { # nolint: object_name_length
|
|
| 259 | -! | +||
| 195 | +270x |
- checkmate::check_string(input_id)+ checkmate::assert_multi_class(modules, c("teal_module", "teal_modules"))
|
|
| 260 | -! | +||
| 196 | +270x |
- self$get_value(input = sprintf("%s-%s", self$active_module_ns(), input_id))
+ checkmate::assert_character(datanames) |
|
| 261 | -+ | ||
| 197 | +270x |
- },+ if (inherits(modules, "teal_modules")) {
|
|
| 262 | -+ | ||
| 198 | +77x |
- #' @description+ unlist( |
|
| 263 | -+ | ||
| 199 | +77x |
- #' Get the output from the module in the `teal` app.+ lapply(modules$children, check_modules_datanames_recursive, datanames = datanames), |
|
| 264 | -+ | ||
| 200 | +77x |
- #' This function will only access outputs from the name space of the current active teal module.+ recursive = FALSE |
|
| 265 | +201 |
- #'+ ) |
|
| 266 | +202 |
- #' @param output_id (character) The shiny output id to get the value from.+ } else {
|
|
| 267 | -+ | ||
| 203 | +193x |
- #'+ missing_datanames <- setdiff(modules$datanames, c("all", datanames))
|
|
| 268 | -+ | ||
| 204 | +193x |
- #' @return The value of the shiny output.+ if (length(missing_datanames)) {
|
|
| 269 | -+ | ||
| 205 | +18x |
- get_active_module_output = function(output_id) {
+ list(list( |
|
| 270 | -! | +||
| 206 | +18x |
- checkmate::check_string(output_id)+ label = modules$label, |
|
| 271 | -! | +||
| 207 | +18x |
- self$get_value(output = sprintf("%s-%s", self$active_module_ns(), output_id))
+ missing_datanames = missing_datanames |
|
| 272 | +208 |
- },+ )) |
|
| 273 | +209 |
- #' @description+ } |
|
| 274 | +210 |
- #' Get the output from the module's `teal.widgets::table_with_settings` or `DT::DTOutput` in the `teal` app.+ } |
|
| 275 | +211 |
- #' This function will only access outputs from the name space of the current active teal module.+ } |
|
| 276 | +212 |
- #'+ |
|
| 277 | +213 |
- #' @param table_id (`character(1)`) The id of the table in the active teal module's name space.+ #' Convert character vector to html code separated with commas and "and" |
|
| 278 | +214 |
- #' @param which (integer) If there is more than one table, which should be extracted.+ #' @noRd |
|
| 279 | +215 |
- #' By default it will look for a table that is built using `teal.widgets::table_with_settings`.+ to_html_code_list <- function(x) {
|
|
| 280 | -+ | ||
| 216 | +34x |
- #'+ checkmate::assert_character(x) |
|
| 281 | -+ | ||
| 217 | +34x |
- #' @return The data.frame with table contents.+ do.call( |
|
| 282 | -+ | ||
| 218 | +34x |
- get_active_module_table_output = function(table_id, which = 1) {
+ tagList, |
|
| 283 | -! | +||
| 219 | +34x |
- checkmate::check_number(which, lower = 1)+ lapply(seq_along(x), function(.ix) {
|
|
| 284 | -! | +||
| 220 | +47x |
- checkmate::check_string(table_id)+ tagList( |
|
| 285 | -! | +||
| 221 | +47x |
- table <- rvest::html_table(+ tags$code(x[.ix]), |
|
| 286 | -! | +||
| 222 | +47x |
- self$get_html_rvest(self$active_module_element(table_id)),+ if (.ix != length(x)) {
|
|
| 287 | -! | +||
| 223 | +1x |
- fill = TRUE+ if (.ix == length(x) - 1) tags$span(" and ") else tags$span(", ", .noWS = "before")
|
|
| 288 | +224 |
- )+ } |
|
| 289 | -! | +||
| 225 | +
- if (length(table) == 0) {
+ ) |
||
| 290 | -! | +||
| 226 | +
- data.frame()+ }) |
||
| 291 | +227 |
- } else {
+ ) |
|
| 292 | -! | +||
| 228 | +
- table[[which]]+ } |
||
| 293 | +229 |
- }+ |
|
| 294 | +230 |
- },+ |
|
| 295 | +231 |
- #' @description+ #' Check `datanames` in filters |
|
| 296 | +232 |
- #' Get the output from the module's `teal.widgets::plot_with_settings` in the `teal` app.+ #' |
|
| 297 | +233 |
- #' This function will only access plots from the name space of the current active teal module.- |
- |
| 298 | -- |
- #'+ #' This function checks whether `datanames` in filters correspond to those in `data`, |
|
| 299 | +234 |
- #' @param plot_id (`character(1)`) The id of the plot in the active teal module's name space.+ #' returning character vector with error messages or `TRUE` if all checks pass. |
|
| 300 | +235 |
- #'+ #' |
|
| 301 | +236 |
- #' @return The `src` attribute as `character(1)` vector.+ #' @param filters (`teal_slices`) object |
|
| 302 | +237 |
- get_active_module_plot_output = function(plot_id) {
- |
- |
| 303 | -! | -
- checkmate::check_string(plot_id)- |
- |
| 304 | -! | -
- self$get_attr(- |
- |
| 305 | -! | -
- self$active_module_element(sprintf("%s-plot_main > img", plot_id)),
- |
- |
| 306 | -! | -
- "src"+ #' @param datanames (`character`) names of datasets available in the `data` object |
|
| 307 | +238 |
- )+ #' |
|
| 308 | +239 |
- },+ #' @return A `character(1)` containing error message or TRUE if validation passes. |
|
| 309 | +240 |
- #' @description+ #' @keywords internal |
|
| 310 | +241 |
- #' Set the input in the module in the `teal` app.+ check_filter_datanames <- function(filters, datanames) {
|
|
| 311 | -+ | ||
| 242 | +77x |
- #' This function will only set inputs in the name space of the current active teal module.+ checkmate::assert_class(filters, "teal_slices") |
|
| 312 | -+ | ||
| 243 | +77x |
- #'+ checkmate::assert_character(datanames) |
|
| 313 | +244 |
- #' @param input_id (character) The shiny input id to get the value from.+ |
|
| 314 | +245 |
- #' @param value The value to set the input to.+ # check teal_slices against datanames |
|
| 315 | -+ | ||
| 246 | +77x |
- #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$set_inputs`+ out <- unlist(sapply( |
|
| 316 | -+ | ||
| 247 | +77x |
- #'+ filters, function(filter) {
|
|
| 317 | -+ | ||
| 248 | +24x |
- #' @return The `TealAppDriver` object invisibly.+ dataname <- shiny::isolate(filter$dataname) |
|
| 318 | -+ | ||
| 249 | +24x |
- set_active_module_input = function(input_id, value, ...) {
+ if (!dataname %in% datanames) {
|
|
| 319 | -! | +||
| 250 | +3x |
- checkmate::check_string(input_id)+ sprintf( |
|
| 320 | -! | +||
| 251 | +3x |
- checkmate::check_string(value)+ "- Filter '%s' refers to dataname not available in 'data':\n %s not in (%s)", |
|
| 321 | -! | +||
| 252 | +3x |
- self$set_input(+ shiny::isolate(filter$id), |
|
| 322 | -! | +||
| 253 | +3x |
- sprintf("%s-%s", self$active_module_ns(), input_id),
+ dQuote(dataname, q = FALSE), |
|
| 323 | -! | +||
| 254 | +3x |
- value,+ toString(dQuote(datanames, q = FALSE)) |
|
| 324 | +255 |
- ...+ ) |
|
| 325 | +256 |
- )- |
- |
| 326 | -! | -
- dots <- rlang::list2(...)- |
- |
| 327 | -! | -
- if (!isFALSE(dots[["wait"]])) self$wait_for_idle() # Default behavior is to wait- |
- |
| 328 | -! | -
- invisible(self)+ } |
|
| 329 | +257 |
- },+ } |
|
| 330 | +258 |
- #' @description+ )) |
|
| 331 | +259 |
- #' Get the active datasets that can be accessed via the filter panel of the current active teal module.+ |
|
| 332 | +260 |
- get_active_filter_vars = function() {
- |
- |
| 333 | -! | -
- displayed_datasets_index <- self$is_visible(+ |
|
| 334 | -! | +||
| 261 | +77x |
- sprintf("#%s-filters-filter_active_vars_contents > span", self$active_filters_ns())
+ if (length(out)) {
|
|
| 335 | -+ | ||
| 262 | +3x |
- )+ paste(out, collapse = "\n") |
|
| 336 | +263 | - - | -|
| 337 | -! | -
- available_datasets <- self$get_text(- |
- |
| 338 | -! | -
- sprintf(- |
- |
| 339 | -! | -
- "#%s-filters-filter_active_vars_contents .filter_panel_dataname",+ } else {
|
|
| 340 | -! | +||
| 264 | +74x |
- self$active_filters_ns()+ TRUE |
|
| 341 | +265 |
- )+ } |
|
| 342 | +266 |
- )+ } |
|
| 343 | +267 | ||
| 344 | -! | +||
| 268 | +
- available_datasets[displayed_datasets_index]+ #' Function for validating the title parameter of `teal::init` |
||
| 345 | +269 |
- },+ #' |
|
| 346 | +270 |
- #' @description+ #' Checks if the input of the title from `teal::init` will create a valid title and favicon tag. |
|
| 347 | +271 |
- #' Get the active data summary table+ #' @param shiny_tag (`shiny.tag`) Object to validate for a valid title. |
|
| 348 | +272 |
- #' @return `data.frame`+ #' @keywords internal |
|
| 349 | +273 |
- get_active_data_summary_table = function() {
+ validate_app_title_tag <- function(shiny_tag) {
|
|
| 350 | -! | +||
| 274 | +7x |
- summary_table <- rvest::html_table(+ checkmate::assert_class(shiny_tag, "shiny.tag") |
|
| 351 | -! | +||
| 275 | +7x |
- self$get_html_rvest(self$active_data_summary_element("table")),
+ checkmate::assert_true(shiny_tag$name == "head") |
|
| 352 | -! | +||
| 276 | +6x |
- fill = TRUE+ child_names <- vapply(shiny_tag$children, `[[`, character(1L), "name") |
|
| 353 | -! | +||
| 277 | +6x |
- )[[1]]+ checkmate::assert_subset(c("title", "link"), child_names, .var.name = "child tags")
|
|
| 354 | -+ | ||
| 278 | +4x |
-
+ rel_attr <- shiny_tag$children[[which(child_names == "link")]]$attribs$rel |
|
| 355 | -! | +||
| 279 | +4x |
- col_names <- unlist(summary_table[1, ], use.names = FALSE)+ checkmate::assert_subset( |
|
| 356 | -! | +||
| 280 | +4x |
- summary_table <- summary_table[-1, ]+ rel_attr, |
|
| 357 | -! | +||
| 281 | +4x |
- colnames(summary_table) <- col_names+ c("icon", "shortcut icon"),
|
|
| 358 | -! | +||
| 282 | +4x |
- if (nrow(summary_table) > 0) {
+ .var.name = "Link tag's rel attribute", |
|
| 359 | -! | +||
| 283 | +4x |
- summary_table+ empty.ok = FALSE |
|
| 360 | +284 |
- } else {
+ ) |
|
| 361 | -! | +||
| 285 | +
- NULL+ } |
||
| 362 | +286 |
- }+ |
|
| 363 | +287 |
- },+ #' Build app title with favicon |
|
| 364 | +288 |
- #' @description+ #' |
|
| 365 | +289 |
- #' Test if `DOM` elements are visible on the page with a JavaScript call.+ #' A helper function to create the browser title along with a logo. |
|
| 366 | +290 |
- #' @param selector (`character(1)`) `CSS` selector to check visibility.+ #' |
|
| 367 | +291 |
- #' A `CSS` id will return only one element if the UI is well formed.+ #' @param title (`character`) The browser title for the `teal` app. |
|
| 368 | +292 |
- #' @param content_visibility_auto,opacity_property,visibility_property (`logical(1)`) See more information+ #' @param favicon (`character`) The path for the icon for the title. |
|
| 369 | +293 |
- #' on <https://developer.mozilla.org/en-US/docs/Web/API/Element/checkVisibility>.+ #' The image/icon path can be remote or the static path accessible by `shiny`, like the `www/` |
|
| 370 | +294 |
- #'+ #' |
|
| 371 | +295 |
- #' @return Logical vector with all occurrences of the selector.+ #' @return A `shiny.tag` containing the element that adds the title and logo to the `shiny` app. |
|
| 372 | +296 |
- is_visible = function(selector,+ #' @export |
|
| 373 | +297 |
- content_visibility_auto = FALSE,+ build_app_title <- function( |
|
| 374 | +298 |
- opacity_property = FALSE,+ title = "teal app", |
|
| 375 | +299 |
- visibility_property = FALSE) {
+ favicon = "https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/PNG/nest.png") {
|
|
| 376 | -! | +||
| 300 | +13x |
- checkmate::assert_string(selector)+ checkmate::assert_string(title, null.ok = TRUE) |
|
| 377 | -! | +||
| 301 | +13x |
- checkmate::assert_flag(content_visibility_auto)+ checkmate::assert_string(favicon, null.ok = TRUE) |
|
| 378 | -! | +||
| 302 | +13x |
- checkmate::assert_flag(opacity_property)+ tags$head( |
|
| 379 | -! | +||
| 303 | +13x |
- checkmate::assert_flag(visibility_property)+ tags$title(title), |
|
| 380 | -+ | ||
| 304 | +13x |
-
+ tags$link( |
|
| 381 | -! | +||
| 305 | +13x |
- private$wait_for_page_stability()+ rel = "icon", |
|
| 382 | -+ | ||
| 306 | +13x |
-
+ href = favicon, |
|
| 383 | -! | +||
| 307 | +13x |
- testthat::skip_if_not(+ sizes = "any" |
|
| 384 | -! | +||
| 308 | +
- self$get_js("typeof Element.prototype.checkVisibility === 'function'"),
+ ) |
||
| 385 | -! | +||
| 309 | +
- "Element.prototype.checkVisibility is not supported in the current browser."+ ) |
||
| 386 | +310 |
- )+ } |
|
| 387 | +311 | ||
| 388 | -! | +||
| 312 | +
- unlist(- |
- ||
| 389 | -! | -
- self$get_js(- |
- |
| 390 | -! | -
- sprintf(- |
- |
| 391 | -! | -
- "Array.from(document.querySelectorAll('%s')).map(el => el.checkVisibility({%s, %s, %s}))",
- |
- |
| 392 | -! | -
- selector,+ #' Application ID |
|
| 393 | +313 |
- # Extra parameters- |
- |
| 394 | -! | -
- sprintf("contentVisibilityAuto: %s", tolower(content_visibility_auto)),
- |
- |
| 395 | -! | -
- sprintf("opacityProperty: %s", tolower(opacity_property)),
- |
- |
| 396 | -! | -
- sprintf("visibilityProperty: %s", tolower(visibility_property))
+ #' |
|
| 397 | +314 |
- )+ #' Creates App ID used to match filter snapshots to application. |
|
| 398 | +315 |
- )+ #' |
|
| 399 | +316 |
- )+ #' Calculate app ID that will be used to stamp filter state snapshots. |
|
| 400 | +317 |
- },+ #' App ID is a hash of the app's data and modules. |
|
| 401 | +318 |
- #' @description+ #' See "transferring snapshots" section in ?snapshot. |
|
| 402 | +319 |
- #' Get the active filter variables from a dataset in the `teal` app.+ #' |
|
| 403 | +320 |
- #'+ #' @param data (`teal_data` or `teal_data_module`) as accepted by `init` |
|
| 404 | +321 |
- #' @param dataset_name (character) The name of the dataset to get the filter variables from.+ #' @param modules (`teal_modules`) object as accepted by `init` |
|
| 405 | +322 |
- #' If `NULL`, the filter variables for all the datasets will be returned in a list.+ #' |
|
| 406 | +323 |
- get_active_data_filters = function(dataset_name = NULL) {
+ #' @return A single character string. |
|
| 407 | -! | +||
| 324 | +
- checkmate::check_string(dataset_name, null.ok = TRUE)+ #' |
||
| 408 | -! | +||
| 325 | +
- datasets <- self$get_active_filter_vars()+ #' @keywords internal |
||
| 409 | -! | +||
| 326 | +
- checkmate::assert_subset(dataset_name, datasets)+ create_app_id <- function(data, modules) {
|
||
| 410 | -! | +||
| 327 | +21x |
- active_filters <- lapply(+ checkmate::assert_multi_class(data, c("teal_data", "teal_data_module"))
|
|
| 411 | -! | +||
| 328 | +20x |
- datasets,+ checkmate::assert_class(modules, "teal_modules") |
|
| 412 | -! | +||
| 329 | +
- function(x) {
+
|
||
| 413 | -! | +||
| 330 | +19x |
- var_names <- gsub(+ data <- if (inherits(data, "teal_data")) {
|
|
| 414 | -! | +||
| 331 | +17x |
- pattern = "\\s",+ as.list(teal.code::get_env(data)) |
|
| 415 | -! | +||
| 332 | +19x |
- replacement = "",+ } else if (inherits(data, "teal_data_module")) {
|
|
| 416 | -! | +||
| 333 | +2x |
- self$get_text(+ deparse1(body(data$server)) |
|
| 417 | -! | +||
| 334 | +
- sprintf(+ } |
||
| 418 | -! | +||
| 335 | +19x |
- "#%s-filters-%s .filter-card-varname",+ modules <- lapply(modules, defunction) |
|
| 419 | -! | +||
| 336 | +
- self$active_filters_ns(),+ |
||
| 420 | -! | +||
| 337 | +19x |
- x+ rlang::hash(list(data = data, modules = modules)) |
|
| 421 | +338 |
- )+ } |
|
| 422 | +339 |
- )+ |
|
| 423 | +340 |
- )- |
- |
| 424 | -! | -
- structure(- |
- |
| 425 | -! | -
- lapply(var_names, private$get_active_filter_selection, dataset_name = x),+ #' Go through list and extract bodies of encountered functions as string, recursively. |
|
| 426 | -! | +||
| 341 | +
- names = var_names+ #' @keywords internal |
||
| 427 | +342 |
- )+ #' @noRd |
|
| 428 | +343 |
- }+ defunction <- function(x) {
|
|
| 429 | -+ | ||
| 344 | +229x |
- )+ if (is.list(x)) {
|
|
| 430 | -! | +||
| 345 | +67x |
- names(active_filters) <- datasets+ lapply(x, defunction) |
|
| 431 | -! | +||
| 346 | +162x |
- if (is.null(dataset_name)) {
+ } else if (is.function(x)) {
|
|
| 432 | -! | +||
| 347 | +50x |
- return(active_filters)+ deparse1(body(x)) |
|
| 433 | +348 |
- }+ } else {
|
|
| 434 | -! | +||
| 349 | +112x |
- active_filters[[dataset_name]]+ x |
|
| 435 | +350 |
- },+ } |
|
| 436 | +351 |
- #' @description+ } |
|
| 437 | +352 |
- #' Add a new variable from the dataset to be filtered.+ |
|
| 438 | +353 |
- #'+ #' Get unique labels |
|
| 439 | +354 |
- #' @param dataset_name (character) The name of the dataset to add the filter variable to.+ #' |
|
| 440 | +355 |
- #' @param var_name (character) The name of the variable to add to the filter panel.+ #' Get unique labels for the modules to avoid namespace conflicts. |
|
| 441 | +356 |
- #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$set_inputs`+ #' |
|
| 442 | +357 |
- #'+ #' @param labels (`character`) vector of labels |
|
| 443 | +358 |
- #' @return The `TealAppDriver` object invisibly.+ #' |
|
| 444 | +359 |
- add_filter_var = function(dataset_name, var_name, ...) {
- |
- |
| 445 | -! | -
- checkmate::check_string(dataset_name)+ #' @return (`character`) vector of unique labels |
|
| 446 | -! | +||
| 360 | +
- checkmate::check_string(var_name)+ #' |
||
| 447 | -! | +||
| 361 | +
- private$set_active_ns()+ #' @keywords internal |
||
| 448 | -! | +||
| 362 | +
- self$click(+ get_unique_labels <- function(labels) {
|
||
| 449 | -! | +||
| 363 | +211x |
- selector = sprintf(+ make.unique(gsub("[^[:alnum:]]", "_", tolower(labels)), sep = "_")
|
|
| 450 | -! | +||
| 364 | +
- "#%s-filters-%s-add_filter_icon",+ } |
||
| 451 | -! | +||
| 365 | +
- private$ns$filter_panel,+ |
||
| 452 | -! | +||
| 366 | +
- dataset_name+ #' Remove ANSI escape sequences from a string |
||
| 453 | +367 |
- )+ #' @noRd |
|
| 454 | +368 |
- )+ strip_style <- function(string) {
|
|
| 455 | -! | +||
| 369 | +2x |
- self$set_input(+ checkmate::assert_string(string) |
|
| 456 | -! | +||
| 370 | +
- sprintf(+ |
||
| 457 | -! | +||
| 371 | +2x |
- "%s-filters-%s-%s-filter-var_to_add",+ gsub( |
|
| 458 | -! | +||
| 372 | +2x |
- private$ns$filter_panel,+ "(?:(?:\\x{001b}\\[)|\\x{009b})(?:(?:[0-9]{1,3})?(?:(?:;[0-9]{0,3})*)?[A-M|f-m])|\\x{001b}[A-M]",
|
|
| 459 | -! | +||
| 373 | +
- dataset_name,+ "", |
||
| 460 | -! | +||
| 374 | +2x |
- dataset_name+ string, |
|
| 461 | -+ | ||
| 375 | +2x |
- ),+ perl = TRUE, |
|
| 462 | -! | +||
| 376 | +2x |
- var_name,+ useBytes = TRUE |
|
| 463 | +377 |
- ...+ ) |
|
| 464 | +378 |
- )+ } |
|
| 465 | -! | +
| 1 | +
- invisible(self)+ # FilteredData ------ |
||
| 466 | +2 |
- },+ |
|
| 467 | +3 |
- #' @description+ #' Drive a `teal` application |
|
| 468 | +4 |
- #' Remove an active filter variable of a dataset from the active filter variables panel.+ #' |
|
| 469 | +5 |
- #'+ #' Extension of the `shinytest2::AppDriver` class with methods for |
|
| 470 | +6 |
- #' @param dataset_name (character) The name of the dataset to remove the filter variable from.+ #' driving a teal application for performing interactions for `shinytest2` tests. |
|
| 471 | +7 |
- #' If `NULL`, all the filter variables will be removed.+ #' |
|
| 472 | +8 |
- #' @param var_name (character) The name of the variable to remove from the filter panel.+ #' @keywords internal |
|
| 473 | +9 |
- #' If `NULL`, all the filter variables of the dataset will be removed.+ #' |
|
| 474 | +10 |
- #'+ TealAppDriver <- R6::R6Class( # nolint: object_name. |
|
| 475 | +11 |
- #' @return The `TealAppDriver` object invisibly.+ "TealAppDriver", |
|
| 476 | +12 |
- remove_filter_var = function(dataset_name = NULL, var_name = NULL) {
+ inherit = {
|
|
| 477 | -! | +||
| 13 | +
- checkmate::check_string(dataset_name, null.ok = TRUE)+ if (!requireNamespace("shinytest2", quietly = TRUE)) {
|
||
| 478 | -! | +||
| 14 | +
- checkmate::check_string(var_name, null.ok = TRUE)+ stop("Please install 'shinytest2' package to use this class.")
|
||
| 479 | -! | +||
| 15 | +
- if (is.null(dataset_name)) {
+ } |
||
| 480 | -! | +||
| 16 | +
- remove_selector <- sprintf(+ if (!requireNamespace("rvest", quietly = TRUE)) {
|
||
| 481 | -! | +||
| 17 | +
- "#%s-active-remove_all_filters",+ stop("Please install 'rvest' package to use this class.")
|
||
| 482 | -! | +||
| 18 | +
- self$active_filters_ns()+ } |
||
| 483 | +19 |
- )+ shinytest2::AppDriver |
|
| 484 | -! | +||
| 20 | +
- } else if (is.null(var_name)) {
+ }, |
||
| 485 | -! | +||
| 21 | +
- remove_selector <- sprintf(+ # public methods ---- |
||
| 486 | -! | +||
| 22 | +
- "#%s-active-%s-remove_filters",+ public = list( |
||
| 487 | -! | +||
| 23 | +
- self$active_filters_ns(),+ #' @description |
||
| 488 | -! | +||
| 24 | +
- dataset_name+ #' Initialize a `TealAppDriver` object for testing a `teal` application. |
||
| 489 | +25 |
- )+ #' |
|
| 490 | +26 |
- } else {
+ #' @param data,modules,filter,title,header,footer,landing_popup arguments passed to `init` |
|
| 491 | -! | +||
| 27 | +
- remove_selector <- sprintf(+ #' @param timeout (`numeric`) Default number of milliseconds for any timeout or |
||
| 492 | -! | +||
| 28 | +
- "#%s-active-%s-filter-%s_%s-remove",+ #' timeout_ parameter in the `TealAppDriver` class. |
||
| 493 | -! | +||
| 29 | +
- self$active_filters_ns(),+ #' Defaults to 20s. |
||
| 494 | -! | +||
| 30 | +
- dataset_name,+ #' |
||
| 495 | -! | +||
| 31 | +
- dataset_name,+ #' See [`shinytest2::AppDriver`] `new` method for more details on how to change it |
||
| 496 | -! | +||
| 32 | +
- var_name+ #' via options or environment variables. |
||
| 497 | +33 |
- )+ #' @param load_timeout (`numeric`) How long to wait for the app to load, in ms. |
|
| 498 | +34 |
- }+ #' This includes the time to start R. Defaults to 100s. |
|
| 499 | -! | +||
| 35 | +
- self$click(+ #' |
||
| 500 | -! | +||
| 36 | +
- selector = remove_selector+ #' See [`shinytest2::AppDriver`] `new` method for more details on how to change it |
||
| 501 | +37 |
- )+ #' via options or environment variables |
|
| 502 | -! | +||
| 38 | +
- invisible(self)+ #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$new` |
||
| 503 | +39 |
- },+ #' |
|
| 504 | +40 |
- #' @description+ #' |
|
| 505 | +41 |
- #' Set the active filter values for a variable of a dataset in the active filter variable panel.+ #' @return Object of class `TealAppDriver` |
|
| 506 | +42 |
- #'+ initialize = function(data, |
|
| 507 | +43 |
- #' @param dataset_name (character) The name of the dataset to set the filter value for.+ modules, |
|
| 508 | +44 |
- #' @param var_name (character) The name of the variable to set the filter value for.+ filter = teal_slices(), |
|
| 509 | +45 |
- #' @param input The value to set the filter to.+ title = build_app_title(), |
|
| 510 | +46 |
- #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$set_inputs`+ header = tags$p(), |
|
| 511 | +47 |
- #'+ footer = tags$p(), |
|
| 512 | +48 |
- #' @return The `TealAppDriver` object invisibly.+ landing_popup = NULL, |
|
| 513 | +49 |
- set_active_filter_selection = function(dataset_name,+ timeout = rlang::missing_arg(), |
|
| 514 | +50 |
- var_name,+ load_timeout = rlang::missing_arg(), |
|
| 515 | +51 |
- input,+ ...) {
|
|
| 516 | -+ | ||
| 52 | +! |
- ...) {
+ private$data <- data |
|
| 517 | +53 | ! |
- checkmate::check_string(dataset_name)+ private$modules <- modules |
| 518 | +54 | ! |
- checkmate::check_string(var_name)+ private$filter <- filter |
| 519 | +55 | ! |
- checkmate::check_string(input)+ app <- init( |
| 520 | -+ | ||
| 56 | +! |
-
+ data = data, |
|
| 521 | +57 | ! |
- input_id_prefix <- sprintf(+ modules = modules, |
| 522 | +58 | ! |
- "%s-filters-%s-filter-%s_%s-inputs",+ filter = filter, |
| 523 | +59 | ! |
- self$active_filters_ns(),+ title = title, |
| 524 | +60 | ! |
- dataset_name,+ header = header, |
| 525 | +61 | ! |
- dataset_name,+ footer = footer, |
| 526 | +62 | ! |
- var_name+ landing_popup = landing_popup, |
| 527 | +63 |
) |
|
| 528 | +64 | ||
| 529 | +65 |
- # Find the type of filter (based on filter panel)+ # Default timeout is hardcoded to 4s in shinytest2:::resolve_timeout |
|
| 530 | -! | +||
| 66 | +
- supported_suffix <- c("selection", "selection_manual")
+ # It must be set as parameter to the AppDriver |
||
| 531 | +67 | ! |
- slices_suffix <- supported_suffix[+ suppressWarnings( |
| 532 | +68 | ! |
- match(+ super$initialize( |
| 533 | +69 | ! |
- TRUE,+ app_dir = shinyApp(app$ui, app$server), |
| 534 | +70 | ! |
- vapply(+ name = "teal", |
| 535 | +71 | ! |
- supported_suffix,+ variant = shinytest2::platform_variant(), |
| 536 | +72 | ! |
- function(suffix) {
+ timeout = rlang::maybe_missing(timeout, 20 * 1000), |
| 537 | +73 | ! |
- !is.null(self$get_html(sprintf("#%s-%s", input_id_prefix, suffix)))
+ load_timeout = rlang::maybe_missing(load_timeout, 100 * 1000), |
| 538 | +74 |
- },- |
- |
| 539 | -! | -
- logical(1)+ ... |
|
| 540 | +75 |
- )+ ) |
|
| 541 | +76 |
- )+ ) |
|
| 542 | +77 |
- ]+ |
|
| 543 | +78 |
-
+ # Check for minimum version of Chrome that supports the tests |
|
| 544 | +79 |
- # Generate correct namespace+ # - Element.checkVisibility was added on 105 |
|
| 545 | +80 | ! |
- slices_input_id <- sprintf(+ chrome_version <- numeric_version( |
| 546 | +81 | ! |
- "%s-filters-%s-filter-%s_%s-inputs-%s",+ gsub( |
| 547 | +82 | ! |
- self$active_filters_ns(),+ "[[:alnum:]_]+/", # Prefix that ends with forward slash |
| 548 | -! | +||
| 83 | +
- dataset_name,+ "", |
||
| 549 | +84 | ! |
- dataset_name,+ self$get_chromote_session()$Browser$getVersion()$product |
| 550 | -! | +||
| 85 | +
- var_name,+ ), |
||
| 551 | +86 | ! |
- slices_suffix+ strict = FALSE |
| 552 | +87 |
) |
|
| 553 | +88 | ||
| 554 | -! | -
- if (identical(slices_suffix, "selection_manual")) {
- |
- |
| 555 | +89 | ! |
- checkmate::assert_numeric(input, len = 2)+ required_version <- "121" |
| 556 | +90 | ||
| 557 | +91 | ! |
- dots <- rlang::list2(...)+ testthat::skip_if( |
| 558 | +92 | ! |
- checkmate::assert_choice(dots$priority_, formals(self$set_inputs)[["priority_"]], null.ok = TRUE)+ is.na(chrome_version), |
| 559 | +93 | ! |
- checkmate::assert_flag(dots$wait_, null.ok = TRUE)+ "Problem getting Chrome version, please contact the developers." |
| 560 | +94 |
-
+ ) |
|
| 561 | +95 | ! |
- self$run_js(+ testthat::skip_if( |
| 562 | +96 | ! |
- sprintf(+ chrome_version < required_version, |
| 563 | +97 | ! |
- "Shiny.setInputValue('%s:sw.numericRange', [%f, %f], {priority: '%s'})",
+ sprintf( |
| 564 | +98 | ! |
- slices_input_id,+ "Chrome version '%s' is not supported, please upgrade to '%s' or higher", |
| 565 | +99 | ! |
- input[[1]],+ chrome_version, |
| 566 | +100 | ! |
- input[[2]],+ required_version |
| 567 | -! | +||
| 101 | +
- priority_ = ifelse(is.null(dots$priority_), "input", dots$priority_)+ ) |
||
| 568 | +102 |
- )+ ) |
|
| 569 | +103 |
- )+ # end od check |
|
| 570 | +104 | ||
| 571 | +105 | ! |
- if (isTRUE(dots$wait_) || is.null(dots$wait_)) {
+ private$set_active_ns() |
| 572 | +106 | ! |
- self$wait_for_idle(+ self$wait_for_idle() |
| 573 | -! | +||
| 107 | +
- timeout = if (is.null(dots$timeout_)) rlang::missing_arg() else dots$timeout_+ }, |
||
| 574 | +108 |
- )+ #' @description |
|
| 575 | +109 |
- }+ #' Append parent [`shinytest2::AppDriver`] `click` method with a call to `waif_for_idle()` method. |
|
| 576 | -! | +||
| 110 | +
- } else if (identical(slices_suffix, "selection")) {
+ #' @param ... arguments passed to parent [`shinytest2::AppDriver`] `click()` method. |
||
| 577 | -! | -
- self$set_input(+ | |
| 111 | ++ |
+ click = function(...) {
|
|
| 578 | +112 | ! |
- slices_input_id,+ super$click(...) |
| 579 | +113 | ! |
- input,+ private$wait_for_page_stability() |
| 580 | +114 |
- ...+ }, |
|
| 581 | +115 |
- )+ #' @description |
|
| 582 | +116 |
- } else {
+ #' Check if the app has shiny errors. This checks for global shiny errors. |
|
| 583 | -! | +||
| 117 | +
- stop("Filter selection set not supported for this slice.")
+ #' Note that any shiny errors dependent on shiny server render will only be captured after the teal module tab |
||
| 584 | +118 |
- }+ #' is visited because shiny will not trigger server computations when the tab is invisible. |
|
| 585 | +119 |
-
+ #' So, navigate to the module tab you want to test before calling this function.+ |
+ |
| 120 | ++ |
+ #' Although, this catches errors hidden in the other module tabs if they are already rendered.+ |
+ |
| 121 | ++ |
+ expect_no_shiny_error = function() {
|
|
| 586 | +122 | ! |
- invisible(self)+ testthat::expect_null(+ |
+
| 123 | +! | +
+ self$get_html(".shiny-output-error:not(.shiny-output-error-validation)"),
+ |
+ |
| 124 | +! | +
+ info = "Shiny error is observed" |
|
| 587 | +125 | ++ |
+ )+ |
+
| 126 |
}, |
||
| 588 | +127 |
#' @description |
|
| 589 | +128 |
- #' Extract `html` attribute (found by a `selector`).+ #' Check if the app has no validation errors. This checks for global shiny validation errors. |
|
| 590 | +129 |
- #'+ expect_no_validation_error = function() {
+ |
+ |
| 130 | +! | +
+ testthat::expect_null(+ |
+ |
| 131 | +! | +
+ self$get_html(".shiny-output-error-validation"),
+ |
+ |
| 132 | +! | +
+ info = "No validation error is observed" |
|
| 591 | +133 |
- #' @param selector (`character(1)`) specifying the selector to be used to get the content of a specific node.+ ) |
|
| 592 | +134 |
- #' @param attribute (`character(1)`) name of an attribute to retrieve from a node specified by `selector`.+ }, |
|
| 593 | +135 |
- #'+ #' @description |
|
| 594 | +136 |
- #' @return The `character` vector.+ #' Check if the app has validation errors. This checks for global shiny validation errors. |
|
| 595 | +137 |
- get_attr = function(selector, attribute) {
+ expect_validation_error = function() {
|
|
| 596 | +138 | ! |
- rvest::html_attr(+ testthat::expect_false( |
| 597 | +139 | ! |
- rvest::html_nodes(self$get_html_rvest("html"), selector),
+ is.null(self$get_html(".shiny-output-error-validation")),
|
| 598 | +140 | ! |
- attribute+ info = "Validation error is not observed" |
| 599 | +141 |
) |
|
| 600 | +142 |
}, |
|
| 601 | +143 |
#' @description |
|
| 602 | +144 |
- #' Wrapper around `get_html` that passes the output directly to `rvest::read_html`.+ #' Set the input in the `teal` app. |
|
| 603 | +145 |
#' |
|
| 604 | +146 |
- #' @param selector `(character(1))` passed to `get_html`.+ #' @param input_id (character) The shiny input id with it's complete name space. |
|
| 605 | +147 |
- #'+ #' @param value The value to set the input to. |
|
| 606 | +148 |
- #' @return An XML document.+ #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$set_inputs` |
|
| 607 | +149 |
- get_html_rvest = function(selector) {
+ #' |
|
| 608 | -! | +||
| 150 | +
- rvest::read_html(self$get_html(selector))+ #' @return The `TealAppDriver` object invisibly. |
||
| 609 | +151 |
- },+ set_input = function(input_id, value, ...) {
|
|
| 610 | -+ | ||
| 152 | +! |
- #' Wrapper around `get_url()` method that opens the app in the browser.+ do.call( |
|
| 611 | -+ | ||
| 153 | +! |
- #'+ self$set_inputs, |
|
| 612 | -+ | ||
| 154 | +! |
- #' @return Nothing. Opens the underlying teal app in the browser.+ c(setNames(list(value), input_id), list(...)) |
|
| 613 | +155 |
- open_url = function() {
+ ) |
|
| 614 | +156 | ! |
- browseURL(self$get_url())+ invisible(self) |
| 615 | +157 |
}, |
|
| 616 | +158 |
#' @description |
|
| 617 | +159 |
- #' Waits until a specified input, output, or export value.+ #' Navigate the teal tabs in the `teal` app. |
|
| 618 | +160 |
- #' This function serves as a wrapper around the `wait_for_value` method,+ #' |
|
| 619 | +161 |
- #' providing a more flexible interface for waiting on different types of values within the active module namespace.+ #' @param tabs (character) Labels of tabs to navigate to. The order of the tabs is important, |
|
| 620 | +162 |
- #' @param input,output,export A name of an input, output, or export value.+ #' and it should start with the most parent level tab. |
|
| 621 | +163 |
- #' Only one of these parameters may be used.+ #' Note: In case the teal tab group has duplicate names, the first tab will be selected, |
|
| 622 | +164 |
- #' @param ... Must be empty. Allows for parameter expansion.+ #' If you wish to select the second tab with the same name, use the suffix "_1". |
|
| 623 | +165 |
- #' Parameter with additional value to passed in `wait_for_value`.+ #' If you wish to select the third tab with the same name, use the suffix "_2" and so on. |
|
| 624 | +166 |
- wait_for_active_module_value = function(input = rlang::missing_arg(),+ #' |
|
| 625 | +167 |
- output = rlang::missing_arg(),+ #' @return The `TealAppDriver` object invisibly. |
|
| 626 | +168 |
- export = rlang::missing_arg(),+ navigate_teal_tab = function(tabs) {
|
|
| 627 | -+ | ||
| 169 | +! |
- ...) {
+ checkmate::check_character(tabs, min.len = 1) |
|
| 628 | +170 | ! |
- ns <- shiny::NS(self$active_module_ns())+ for (tab in tabs) {
|
| 629 | -+ | ||
| 171 | +! |
-
+ self$set_input( |
|
| 630 | +172 | ! |
- if (!rlang::is_missing(input) && checkmate::test_string(input, min.chars = 1)) input <- ns(input)+ "teal-teal_modules-active_tab", |
| 631 | +173 | ! |
- if (!rlang::is_missing(output) && checkmate::test_string(output, min.chars = 1)) output <- ns(output)+ get_unique_labels(tab), |
| 632 | +174 | ! |
- if (!rlang::is_missing(export) && checkmate::test_string(export, min.chars = 1)) export <- ns(export)+ wait_ = FALSE |
| 633 | +175 |
-
+ ) |
|
| 634 | -! | +||
| 176 | +
- self$wait_for_value(+ } |
||
| 635 | +177 | ! |
- input = input,+ self$wait_for_idle() |
| 636 | +178 | ! |
- output = output,+ private$set_active_ns() |
| 637 | +179 | ! |
- export = export,+ invisible(self) |
| 638 | +180 |
- ...+ }, |
|
| 639 | +181 |
- )+ #' @description |
|
| 640 | +182 |
- }+ #' Get the active shiny name space for different components of the teal app. |
|
| 641 | +183 |
- ),+ #' |
|
| 642 | +184 |
- # private members ----+ #' @return (`list`) The list of active shiny name space of the teal components. |
|
| 643 | +185 |
- private = list(+ active_ns = function() {
|
|
| 644 | -+ | ||
| 186 | +! |
- # private attributes ----+ if (identical(private$ns$module, character(0))) {
|
|
| 645 | -+ | ||
| 187 | +! |
- data = NULL,+ private$set_active_ns() |
|
| 646 | +188 |
- modules = NULL,+ } |
|
| 647 | -+ | ||
| 189 | +! |
- filter = teal_slices(),+ private$ns |
|
| 648 | +190 |
- ns = list(+ }, |
|
| 649 | +191 |
- module = character(0),+ #' @description |
|
| 650 | +192 |
- filter_panel = character(0)+ #' Get the active shiny name space for interacting with the module content. |
|
| 651 | +193 |
- ),+ #' |
|
| 652 | +194 |
- # private methods ----+ #' @return (`string`) The active shiny name space of the component. |
|
| 653 | +195 |
- set_active_ns = function() {
+ active_module_ns = function() {
|
|
| 654 | +196 | ! |
- all_inputs <- self$get_values()$input+ if (identical(private$ns$module, character(0))) {
|
| 655 | +197 | ! |
- active_tab_inputs <- all_inputs[grepl("-active_tab$", names(all_inputs))]
+ private$set_active_ns() |
| 656 | +198 |
-
+ } |
|
| 657 | +199 | ! |
- tab_ns <- unlist(lapply(names(active_tab_inputs), function(name) {
+ private$ns$module |
| 658 | -! | +||
| 200 | +
- gsub(+ }, |
||
| 659 | -! | +||
| 201 | +
- pattern = "-active_tab$",+ #' @description |
||
| 660 | -! | +||
| 202 | +
- replacement = sprintf("-%s", active_tab_inputs[[name]]),
+ #' Get the active shiny name space bound with a custom `element` name. |
||
| 661 | -! | +||
| 203 | +
- name+ #' |
||
| 662 | +204 |
- )+ #' @param element `character(1)` custom element name. |
|
| 663 | +205 |
- }))+ #' |
|
| 664 | -! | +||
| 206 | +
- active_ns <- tab_ns[1]+ #' @return (`string`) The active shiny name space of the component bound with the input `element`. |
||
| 665 | -! | +||
| 207 | +
- if (length(tab_ns) > 1) {
+ active_module_element = function(element) {
|
||
| 666 | +208 | ! |
- for (i in 2:length(tab_ns)) {
+ checkmate::assert_string(element) |
| 667 | +209 | ! |
- next_ns <- tab_ns[i]+ sprintf("#%s-%s", self$active_module_ns(), element)
|
| 668 | -! | +||
| 210 | +
- if (grepl(pattern = active_ns, next_ns)) {
+ }, |
||
| 669 | -! | +||
| 211 | +
- active_ns <- next_ns+ #' @description |
||
| 670 | +212 |
- }+ #' Get the text of the active shiny name space bound with a custom `element` name. |
|
| 671 | +213 |
- }+ #' |
|
| 672 | +214 |
- }+ #' @param element `character(1)` the text of the custom element name. |
|
| 673 | -! | +||
| 215 | +
- private$ns$module <- sprintf("%s-%s", active_ns, "module")
+ #' |
||
| 674 | +216 | - - | -|
| 675 | -! | -
- components <- c("filter_panel", "data_summary")
- |
- |
| 676 | -! | -
- for (component in components) {
+ #' @return (`string`) The text of the active shiny name space of the component bound with the input `element`. |
|
| 677 | +217 |
- if (+ active_module_element_text = function(element) {
|
|
| 678 | +218 | ! |
- !is.null(self$get_html(sprintf("#%s-%s-panel", active_ns, component))) ||
+ checkmate::assert_string(element) |
| 679 | +219 | ! |
- !is.null(self$get_html(sprintf("#%s-%s-table", active_ns, component)))
+ self$get_text(self$active_module_element(element)) |
| 680 | +220 |
- ) {
+ }, |
|
| 681 | -! | +||
| 221 | +
- private$ns[[component]] <- sprintf("%s-%s", active_ns, component)
+ #' @description |
||
| 682 | +222 |
- } else {
+ #' Get the active shiny name space for interacting with the filter panel. |
|
| 683 | -! | +||
| 223 | +
- private$ns[[component]] <- sprintf("%s-module_%s", active_ns, component)
+ #' |
||
| 684 | +224 |
- }+ #' @return (`string`) The active shiny name space of the component. |
|
| 685 | +225 |
- }+ active_filters_ns = function() {
|
|
| 686 | -+ | ||
| 226 | +! |
- },+ if (identical(private$ns$filter_panel, character(0))) {
|
|
| 687 | -+ | ||
| 227 | +! |
- # @description+ private$set_active_ns() |
|
| 688 | +228 |
- # Get the active filter values from the active filter selection of dataset from the filter panel.+ } |
|
| 689 | -+ | ||
| 229 | +! |
- #+ private$ns$filter_panel |
|
| 690 | +230 |
- # @param dataset_name (character) The name of the dataset to get the filter values from.+ }, |
|
| 691 | +231 |
- # @param var_name (character) The name of the variable to get the filter values from.+ #' @description |
|
| 692 | +232 |
- #+ #' Get the active shiny name space for interacting with the data-summary panel. |
|
| 693 | +233 |
- # @return The value of the active filter selection.+ #' |
|
| 694 | +234 |
- get_active_filter_selection = function(dataset_name, var_name) {
+ #' @return (`string`) The active shiny name space of the data-summary component. |
|
| 695 | -! | +||
| 235 | +
- checkmate::check_string(dataset_name)+ active_data_summary_ns = function() {
|
||
| 696 | +236 | ! |
- checkmate::check_string(var_name)+ if (identical(private$ns$data_summary, character(0))) {
|
| 697 | +237 | ! |
- input_id_prefix <- sprintf(+ private$set_active_ns() |
| 698 | -! | +||
| 238 | +
- "%s-filters-%s-filter-%s_%s-inputs",+ } |
||
| 699 | +239 | ! |
- self$active_filters_ns(),+ private$ns$data_summary |
| 700 | -! | +||
| 240 | +
- dataset_name,+ }, |
||
| 701 | -! | +||
| 241 | +
- dataset_name,+ #' @description |
||
| 702 | -! | +||
| 242 | +
- var_name+ #' Get the active shiny name space bound with a custom `element` name. |
||
| 703 | +243 |
- )+ #' |
|
| 704 | +244 |
-
+ #' @param element `character(1)` custom element name. |
|
| 705 | +245 |
- # Find the type of filter (categorical or range)+ #' |
|
| 706 | -! | +||
| 246 | +
- supported_suffix <- c("selection", "selection_manual")
+ #' @return (`string`) The active shiny name space of the component bound with the input `element`. |
||
| 707 | -! | +||
| 247 | +
- for (suffix in supported_suffix) {
+ active_data_summary_element = function(element) {
|
||
| 708 | +248 | ! |
- if (!is.null(self$get_html(sprintf("#%s-%s", input_id_prefix, suffix)))) {
+ checkmate::assert_string(element) |
| 709 | +249 | ! |
- return(self$get_value(input = sprintf("%s-%s", input_id_prefix, suffix)))
- |
-
| 710 | -- |
- }+ sprintf("#%s-%s", self$active_data_summary_ns(), element)
|
|
| 711 | +250 |
- }+ }, |
|
| 712 | +251 | - - | -|
| 713 | -! | -
- NULL # If there are not any supported filters+ #' @description |
|
| 714 | +252 |
- },+ #' Get the input from the module in the `teal` app. |
|
| 715 | +253 |
- # @description+ #' This function will only access inputs from the name space of the current active teal module. |
|
| 716 | +254 |
- # Check if the page is stable without any `DOM` updates in the body of the app.+ #' |
|
| 717 | +255 |
- # This is achieved by blocing the R process by sleeping until the page is unchanged till the `stability_period`.+ #' @param input_id (character) The shiny input id to get the value from. |
|
| 718 | +256 |
- # @param stability_period (`numeric(1)`) The time in milliseconds to wait till the page to be stable.+ #' |
|
| 719 | +257 |
- # @param check_interval (`numeric(1)`) The time in milliseconds to check for changes in the page.+ #' @return The value of the shiny input. |
|
| 720 | +258 |
- # The stability check is reset when a change is detected in the page after sleeping for check_interval.+ get_active_module_input = function(input_id) {
|
|
| 721 | -+ | ||
| 259 | +! |
- wait_for_page_stability = function(stability_period = 2000, check_interval = 200) {
+ checkmate::check_string(input_id) |
|
| 722 | +260 | ! |
- previous_content <- self$get_html("body")
+ self$get_value(input = sprintf("%s-%s", self$active_module_ns(), input_id))
|
| 723 | -! | +||
| 261 | +
- end_time <- Sys.time() + (stability_period / 1000)+ }, |
||
| 724 | +262 |
-
+ #' @description |
|
| 725 | -! | +||
| 263 | +
- repeat {
+ #' Get the output from the module in the `teal` app. |
||
| 726 | -! | +||
| 264 | +
- Sys.sleep(check_interval / 1000)+ #' This function will only access outputs from the name space of the current active teal module. |
||
| 727 | -! | +||
| 265 | +
- current_content <- self$get_html("body")
+ #' |
||
| 728 | +266 |
-
+ #' @param output_id (character) The shiny output id to get the value from. |
|
| 729 | -! | +||
| 267 | +
- if (!identical(previous_content, current_content)) {
+ #' |
||
| 730 | -! | +||
| 268 | +
- previous_content <- current_content+ #' @return The value of the shiny output. |
||
| 731 | -! | +||
| 269 | +
- end_time <- Sys.time() + (stability_period / 1000)+ get_active_module_output = function(output_id) {
|
||
| 732 | +270 | ! |
- } else if (Sys.time() >= end_time) {
+ checkmate::check_string(output_id) |
| 733 | +271 | ! |
- break+ self$get_value(output = sprintf("%s-%s", self$active_module_ns(), output_id))
|
| 734 | +272 |
- }+ }, |
|
| 735 | +273 |
- }+ #' @description |
|
| 736 | +274 |
- }+ #' Get the output from the module's `teal.widgets::table_with_settings` or `DT::DTOutput` in the `teal` app. |
|
| 737 | +275 |
- )+ #' This function will only access outputs from the name space of the current active teal module. |
|
| 738 | +276 |
- )+ #' |
| 1 | +277 |
- setOldClass("teal_module")
+ #' @param table_id (`character(1)`) The id of the table in the active teal module's name space. |
|
| 2 | +278 |
- setOldClass("teal_modules")
+ #' @param which (integer) If there is more than one table, which should be extracted. |
|
| 3 | +279 |
-
+ #' By default it will look for a table that is built using `teal.widgets::table_with_settings`. |
|
| 4 | +280 |
- #' Create `teal_module` and `teal_modules` objects+ #' |
|
| 5 | +281 |
- #'+ #' @return The data.frame with table contents. |
|
| 6 | +282 |
- #' @description+ get_active_module_table_output = function(table_id, which = 1) {
|
|
| 7 | -+ | ||
| 283 | +! |
- #' `r lifecycle::badge("stable")`
+ checkmate::check_number(which, lower = 1) |
|
| 8 | -+ | ||
| 284 | +! |
- #' Create a nested tab structure to embed modules in a `teal` application.+ checkmate::check_string(table_id) |
|
| 9 | -+ | ||
| 285 | +! |
- #'+ table <- rvest::html_table( |
|
| 10 | -+ | ||
| 286 | +! |
- #' @details+ self$get_html_rvest(self$active_module_element(table_id)), |
|
| 11 | -+ | ||
| 287 | +! |
- #' `module()` creates an instance of a `teal_module` that can be placed in a `teal` application.+ fill = TRUE |
|
| 12 | +288 |
- #' `modules()` shapes the structure of a the application by organizing `teal_module` within the navigation panel.+ ) |
|
| 13 | -+ | ||
| 289 | +! |
- #' It wraps `teal_module` and `teal_modules` objects in a `teal_modules` object,+ if (length(table) == 0) {
|
|
| 14 | -+ | ||
| 290 | +! |
- #' which results in a nested structure corresponding to the nested tabs in the final application.+ data.frame() |
|
| 15 | +291 |
- #'+ } else {
|
|
| 16 | -+ | ||
| 292 | +! |
- #' Note that for `modules()` `label` comes after `...`, so it must be passed as a named argument,+ table[[which]] |
|
| 17 | +293 |
- #' otherwise it will be captured by `...`.+ } |
|
| 18 | +294 |
- #'+ }, |
|
| 19 | +295 |
- #' The labels `"global_filters"` and `"Report previewer"` are reserved+ #' @description |
|
| 20 | +296 |
- #' because they are used by the `mapping` argument of [teal_slices()]+ #' Get the output from the module's `teal.widgets::plot_with_settings` in the `teal` app. |
|
| 21 | +297 |
- #' and the report previewer module [reporter_previewer_module()], respectively.+ #' This function will only access plots from the name space of the current active teal module. |
|
| 22 | +298 |
- #'+ #' |
|
| 23 | +299 |
- #' # Restricting datasets used by `teal_module`:+ #' @param plot_id (`character(1)`) The id of the plot in the active teal module's name space. |
|
| 24 | +300 |
- #' The `datanames` argument controls which datasets are used by the module’s server. These datasets,+ #' |
|
| 25 | +301 |
- #' passed via server's `data` argument, are the only ones shown in the module's tab.+ #' @return The `src` attribute as `character(1)` vector. |
|
| 26 | +302 |
- #'+ get_active_module_plot_output = function(plot_id) {
|
|
| 27 | -+ | ||
| 303 | +! |
- #' When `datanames` is set to `"all"`, all datasets in the data object are treated as relevant.+ checkmate::check_string(plot_id) |
|
| 28 | -+ | ||
| 304 | +! |
- #' However, this may include unnecessary datasets, such as:+ self$get_attr( |
|
| 29 | -- |
- #' - Proxy variables for column modifications+ | |
| 305 | +! | +
+ self$active_module_element(sprintf("%s-plot_main > img", plot_id)),
|
|
| 30 | -+ | ||
| 306 | +! |
- #' - Temporary datasets used to create final versions+ "src" |
|
| 31 | +307 |
- #' - Connection objects+ ) |
|
| 32 | +308 |
- #'+ }, |
|
| 33 | +309 |
- #' To exclude irrelevant datasets, use the [set_datanames()] function to change `datanames` from+ #' @description |
|
| 34 | +310 |
- #' `"all"` to specific names. Trying to modify non-`"all"` values with [set_datanames()] will result+ #' Set the input in the module in the `teal` app. |
|
| 35 | +311 |
- #' in a warning. Datasets with names starting with . are ignored globally unless explicitly listed+ #' This function will only set inputs in the name space of the current active teal module. |
|
| 36 | +312 |
- #' in `datanames`.+ #' |
|
| 37 | +313 |
- #'+ #' @param input_id (character) The shiny input id to get the value from. |
|
| 38 | +314 |
- #' # `datanames` with `transformers`+ #' @param value The value to set the input to. |
|
| 39 | +315 |
- #' When transformers are specified, their `datanames` are added to the module’s `datanames`, which+ #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$set_inputs` |
|
| 40 | +316 |
- #' changes the behavior as follows:+ #' |
|
| 41 | +317 |
- #' - If `module(datanames)` is `NULL` and the `transformers` have defined `datanames`, the sidebar+ #' @return The `TealAppDriver` object invisibly. |
|
| 42 | +318 |
- #' will appear showing the `transformers`' datasets, instead of being hidden.+ set_active_module_input = function(input_id, value, ...) {
|
|
| 43 | -+ | ||
| 319 | +! |
- #' - If `module(datanames)` is set to specific values and any `transformer` has `datanames = "all"`,+ checkmate::check_string(input_id) |
|
| 44 | -+ | ||
| 320 | +! |
- #' the module may receive extra datasets that could be unnecessary+ checkmate::check_string(value) |
|
| 45 | -+ | ||
| 321 | +! |
- #'+ self$set_input( |
|
| 46 | -+ | ||
| 322 | +! |
- #' @param label (`character(1)`) Label shown in the navigation item for the module or module group.+ sprintf("%s-%s", self$active_module_ns(), input_id),
|
|
| 47 | -+ | ||
| 323 | +! |
- #' For `modules()` defaults to `"root"`. See `Details`.+ value, |
|
| 48 | +324 |
- #' @param server (`function`) `shiny` module with following arguments:+ ... |
|
| 49 | +325 |
- #' - `id` - `teal` will set proper `shiny` namespace for this module (see [shiny::moduleServer()]).+ ) |
|
| 50 | -+ | ||
| 326 | +! |
- #' - `input`, `output`, `session` - (optional; not recommended) When provided, then [shiny::callModule()]+ dots <- rlang::list2(...) |
|
| 51 | -+ | ||
| 327 | +! |
- #' will be used to call a module. From `shiny` 1.5.0, the recommended way is to use+ if (!isFALSE(dots[["wait"]])) self$wait_for_idle() # Default behavior is to wait |
|
| 52 | -+ | ||
| 328 | +! |
- #' [shiny::moduleServer()] instead which doesn't require these arguments.+ invisible(self) |
|
| 53 | +329 |
- #' - `data` (optional) When provided, the module will be called with `teal_data` object (i.e. a list of+ }, |
|
| 54 | +330 |
- #' reactive (filtered) data specified in the `filters` argument) as the value of this argument.+ #' @description |
|
| 55 | +331 |
- #' - `datasets` (optional) When provided, the module will be called with `FilteredData` object as the+ #' Get the active datasets that can be accessed via the filter panel of the current active teal module. |
|
| 56 | +332 |
- #' value of this argument. (See [`teal.slice::FilteredData`]).+ get_active_filter_vars = function() {
|
|
| 57 | -+ | ||
| 333 | +! |
- #' - `reporter` (optional) When provided, the module will be called with `Reporter` object as the value+ displayed_datasets_index <- self$is_visible( |
|
| 58 | -+ | ||
| 334 | +! |
- #' of this argument. (See [`teal.reporter::Reporter`]).+ sprintf("#%s-filters-filter_active_vars_contents > span", self$active_filters_ns())
|
|
| 59 | +335 |
- #' - `filter_panel_api` (optional) When provided, the module will be called with `FilterPanelAPI` object+ ) |
|
| 60 | +336 |
- #' as the value of this argument. (See [`teal.slice::FilterPanelAPI`]).+ |
|
| 61 | -+ | ||
| 337 | +! |
- #' - `...` (optional) When provided, `server_args` elements will be passed to the module named argument+ available_datasets <- self$get_text( |
|
| 62 | -+ | ||
| 338 | +! |
- #' or to the `...`.+ sprintf( |
|
| 63 | -+ | ||
| 339 | +! |
- #' @param ui (`function`) `shiny` UI module function with following arguments:+ "#%s-filters-filter_active_vars_contents .filter_panel_dataname", |
|
| 64 | -+ | ||
| 340 | +! |
- #' - `id` - `teal` will set proper `shiny` namespace for this module.+ self$active_filters_ns() |
|
| 65 | +341 |
- #' - `...` (optional) When provided, `ui_args` elements will be passed to the module named argument+ ) |
|
| 66 | +342 |
- #' or to the `...`.+ ) |
|
| 67 | +343 |
- #' @param filters (`character`) Deprecated. Use `datanames` instead.+ |
|
| 68 | -+ | ||
| 344 | +! |
- #' @param datanames (`character`) Names of the datasets relevant to the item.+ available_datasets[displayed_datasets_index] |
|
| 69 | +345 |
- #' There are 2 reserved values that have specific behaviors:+ }, |
|
| 70 | +346 |
- #' - The keyword `"all"` includes all datasets available in the data passed to the teal application.+ #' @description |
|
| 71 | +347 |
- #' - `NULL` hides the sidebar panel completely.+ #' Get the active data summary table |
|
| 72 | +348 |
- #' - If `transformers` are specified, their `datanames` are automatically added to this `datanames`+ #' @return `data.frame` |
|
| 73 | +349 |
- #' argument.+ get_active_data_summary_table = function() {
|
|
| 74 | -+ | ||
| 350 | +! |
- #' @param server_args (named `list`) with additional arguments passed on to the server function.+ summary_table <- rvest::html_table( |
|
| 75 | -+ | ||
| 351 | +! |
- #' @param ui_args (named `list`) with additional arguments passed on to the UI function.+ self$get_html_rvest(self$active_data_summary_element("table")),
|
|
| 76 | -+ | ||
| 352 | +! |
- #' @param x (`teal_module` or `teal_modules`) Object to format/print.+ fill = TRUE |
|
| 77 | -+ | ||
| 353 | +! |
- #' @param indent (`integer(1)`) Indention level; each nested element is indented one level more.+ )[[1]] |
|
| 78 | +354 |
- #' @param transformers (`list` of `teal_data_module`) that will be applied to transform the data.+ |
|
| 79 | -+ | ||
| 355 | +! |
- #' Each transform module UI will appear in the `teal`'s sidebar panel.+ col_names <- unlist(summary_table[1, ], use.names = FALSE) |
|
| 80 | -+ | ||
| 356 | +! |
- #' Transformers' `datanames` are added to the `datanames`. See [teal_transform_module()].+ summary_table <- summary_table[-1, ] |
|
| 81 | -+ | ||
| 357 | +! |
- #'+ colnames(summary_table) <- col_names |
|
| 82 | -+ | ||
| 358 | +! |
- #' @param ...+ if (nrow(summary_table) > 0) {
|
|
| 83 | -+ | ||
| 359 | +! |
- #' - For `modules()`: (`teal_module` or `teal_modules`) Objects to wrap into a tab.+ summary_table |
|
| 84 | +360 |
- #' - For `format()` and `print()`: Arguments passed to other methods.+ } else {
|
|
| 85 | -+ | ||
| 361 | +! |
- #'+ NULL |
|
| 86 | +362 |
- #' @return+ } |
|
| 87 | +363 |
- #' `module()` returns an object of class `teal_module`.+ }, |
|
| 88 | +364 |
- #'+ #' @description |
|
| 89 | +365 |
- #' `modules()` returns a `teal_modules` object which contains following fields:+ #' Test if `DOM` elements are visible on the page with a JavaScript call. |
|
| 90 | +366 |
- #' - `label`: taken from the `label` argument.+ #' @param selector (`character(1)`) `CSS` selector to check visibility. |
|
| 91 | +367 |
- #' - `children`: a list containing objects passed in `...`. List elements are named after+ #' A `CSS` id will return only one element if the UI is well formed. |
|
| 92 | +368 |
- #' their `label` attribute converted to a valid `shiny` id.+ #' @param content_visibility_auto,opacity_property,visibility_property (`logical(1)`) See more information |
|
| 93 | +369 |
- #'+ #' on <https://developer.mozilla.org/en-US/docs/Web/API/Element/checkVisibility>. |
|
| 94 | +370 |
- #' @name teal_modules+ #' |
|
| 95 | +371 |
- #' @aliases teal_module+ #' @return Logical vector with all occurrences of the selector. |
|
| 96 | +372 |
- #'+ is_visible = function(selector, |
|
| 97 | +373 |
- #' @examples+ content_visibility_auto = FALSE, |
|
| 98 | +374 |
- #' library(shiny)+ opacity_property = FALSE, |
|
| 99 | +375 |
- #'+ visibility_property = FALSE) {
|
|
| 100 | -+ | ||
| 376 | +! |
- #' module_1 <- module(+ checkmate::assert_string(selector) |
|
| 101 | -+ | ||
| 377 | +! |
- #' label = "a module",+ checkmate::assert_flag(content_visibility_auto) |
|
| 102 | -+ | ||
| 378 | +! |
- #' server = function(id, data) {
+ checkmate::assert_flag(opacity_property) |
|
| 103 | -+ | ||
| 379 | +! |
- #' moduleServer(+ checkmate::assert_flag(visibility_property) |
|
| 104 | +380 |
- #' id,+ |
|
| 105 | -+ | ||
| 381 | +! |
- #' module = function(input, output, session) {
+ private$wait_for_page_stability() |
|
| 106 | +382 |
- #' output$data <- renderDataTable(data()[["iris"]])+ |
|
| 107 | -+ | ||
| 383 | +! |
- #' }+ testthat::skip_if_not( |
|
| 108 | -+ | ||
| 384 | +! |
- #' )+ self$get_js("typeof Element.prototype.checkVisibility === 'function'"),
|
|
| 109 | -+ | ||
| 385 | +! |
- #' },+ "Element.prototype.checkVisibility is not supported in the current browser." |
|
| 110 | +386 |
- #' ui = function(id) {
+ ) |
|
| 111 | +387 |
- #' ns <- NS(id)+ |
|
| 112 | -+ | ||
| 388 | +! |
- #' tagList(dataTableOutput(ns("data")))
+ unlist( |
|
| 113 | -+ | ||
| 389 | +! |
- #' },+ self$get_js( |
|
| 114 | -+ | ||
| 390 | +! |
- #' datanames = "all"+ sprintf( |
|
| 115 | -+ | ||
| 391 | +! |
- #' )+ "Array.from(document.querySelectorAll('%s')).map(el => el.checkVisibility({%s, %s, %s}))",
|
|
| 116 | -+ | ||
| 392 | +! |
- #'+ selector, |
|
| 117 | +393 |
- #' module_2 <- module(+ # Extra parameters |
|
| 118 | -+ | ||
| 394 | +! |
- #' label = "another module",+ sprintf("contentVisibilityAuto: %s", tolower(content_visibility_auto)),
|
|
| 119 | -+ | ||
| 395 | +! |
- #' server = function(id) {
+ sprintf("opacityProperty: %s", tolower(opacity_property)),
|
|
| 120 | -+ | ||
| 396 | +! |
- #' moduleServer(+ sprintf("visibilityProperty: %s", tolower(visibility_property))
|
|
| 121 | +397 |
- #' id,+ ) |
|
| 122 | +398 |
- #' module = function(input, output, session) {
+ ) |
|
| 123 | +399 |
- #' output$text <- renderText("Another Module")
+ ) |
|
| 124 | +400 |
- #' }+ }, |
|
| 125 | +401 |
- #' )+ #' @description |
|
| 126 | +402 |
- #' },+ #' Get the active filter variables from a dataset in the `teal` app. |
|
| 127 | +403 |
- #' ui = function(id) {
+ #' |
|
| 128 | +404 |
- #' ns <- NS(id)+ #' @param dataset_name (character) The name of the dataset to get the filter variables from. |
|
| 129 | +405 |
- #' tagList(textOutput(ns("text")))
+ #' If `NULL`, the filter variables for all the datasets will be returned in a list. |
|
| 130 | +406 |
- #' },+ get_active_data_filters = function(dataset_name = NULL) {
|
|
| 131 | -+ | ||
| 407 | +! |
- #' datanames = NULL+ checkmate::check_string(dataset_name, null.ok = TRUE) |
|
| 132 | -+ | ||
| 408 | +! |
- #' )+ datasets <- self$get_active_filter_vars() |
|
| 133 | -+ | ||
| 409 | +! |
- #'+ checkmate::assert_subset(dataset_name, datasets) |
|
| 134 | -+ | ||
| 410 | +! |
- #' modules <- modules(+ active_filters <- lapply( |
|
| 135 | -+ | ||
| 411 | +! |
- #' label = "modules",+ datasets, |
|
| 136 | -+ | ||
| 412 | +! |
- #' modules(+ function(x) {
|
|
| 137 | -+ | ||
| 413 | +! |
- #' label = "nested modules",+ var_names <- gsub( |
|
| 138 | -+ | ||
| 414 | +! |
- #' module_1+ pattern = "\\s", |
|
| 139 | -+ | ||
| 415 | +! |
- #' ),+ replacement = "", |
|
| 140 | -+ | ||
| 416 | +! |
- #' module_2+ self$get_text( |
|
| 141 | -+ | ||
| 417 | +! |
- #' )+ sprintf( |
|
| 142 | -+ | ||
| 418 | +! |
- #'+ "#%s-filters-%s .filter-card-varname", |
|
| 143 | -+ | ||
| 419 | +! |
- #' app <- init(+ self$active_filters_ns(), |
|
| 144 | -+ | ||
| 420 | +! |
- #' data = teal_data(iris = iris),+ x |
|
| 145 | +421 |
- #' modules = modules+ ) |
|
| 146 | +422 |
- #' )+ ) |
|
| 147 | +423 |
- #'+ ) |
|
| 148 | -+ | ||
| 424 | +! |
- #' if (interactive()) {
+ structure( |
|
| 149 | -+ | ||
| 425 | +! |
- #' shinyApp(app$ui, app$server)+ lapply(var_names, private$get_active_filter_selection, dataset_name = x),+ |
+ |
| 426 | +! | +
+ names = var_names |
|
| 150 | +427 |
- #' }+ ) |
|
| 151 | +428 |
- #' @rdname teal_modules+ } |
|
| 152 | +429 |
- #' @export+ )+ |
+ |
| 430 | +! | +
+ names(active_filters) <- datasets+ |
+ |
| 431 | +! | +
+ if (is.null(dataset_name)) {
+ |
+ |
| 432 | +! | +
+ return(active_filters) |
|
| 153 | +433 |
- #'+ }+ |
+ |
| 434 | +! | +
+ active_filters[[dataset_name]] |
|
| 154 | +435 |
- module <- function(label = "module",+ }, |
|
| 155 | +436 |
- server = function(id, data, ...) moduleServer(id, function(input, output, session) NULL),+ #' @description |
|
| 156 | +437 |
- ui = function(id, ...) tags$p(paste0("This module has no UI (id: ", id, " )")),
+ #' Add a new variable from the dataset to be filtered. |
|
| 157 | +438 |
- filters,+ #' |
|
| 158 | +439 |
- datanames = "all",+ #' @param dataset_name (character) The name of the dataset to add the filter variable to. |
|
| 159 | +440 |
- server_args = NULL,+ #' @param var_name (character) The name of the variable to add to the filter panel. |
|
| 160 | +441 |
- ui_args = NULL,+ #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$set_inputs` |
|
| 161 | +442 |
- transformers = list()) {
+ #' |
|
| 162 | +443 |
- # argument checking (independent)+ #' @return The `TealAppDriver` object invisibly. |
|
| 163 | +444 |
- ## `label`+ add_filter_var = function(dataset_name, var_name, ...) {
|
|
| 164 | -207x - | +||
| 445 | +! |
- checkmate::assert_string(label)+ checkmate::check_string(dataset_name) |
|
| 165 | -204x - | +||
| 446 | +! |
- if (label == "global_filters") {
+ checkmate::check_string(var_name) |
|
| 166 | -1x - | +||
| 447 | +! |
- stop(+ private$set_active_ns() |
|
| 167 | -1x - | +||
| 448 | +! |
- sprintf("module(label = \"%s\", ...\n ", label),
+ self$click( |
|
| 168 | -1x - | +||
| 449 | +! |
- "Label 'global_filters' is reserved in teal. Please change to something else.",+ selector = sprintf( |
|
| 169 | -1x - | +||
| 450 | +! |
- call. = FALSE+ "#%s-filters-%s-add_filter_icon",+ |
+ |
| 451 | +! | +
+ private$ns$filter_panel,+ |
+ |
| 452 | +! | +
+ dataset_name |
|
| 170 | +453 |
- )+ ) |
|
| 171 | +454 |
- }+ ) |
|
| 172 | -203x - | +||
| 455 | +! |
- if (label == "Report previewer") {
+ self$set_input( |
|
| 173 | +456 | ! |
- stop(+ sprintf( |
| 174 | +457 | ! |
- sprintf("module(label = \"%s\", ...\n ", label),
+ "%s-filters-%s-%s-filter-var_to_add", |
| 175 | +458 | ! |
- "Label 'Report previewer' is reserved in teal. Please change to something else.",+ private$ns$filter_panel, |
| 176 | +459 | ! |
- call. = FALSE+ dataset_name, |
| 177 | -+ | ||
| 460 | +! |
- )+ dataset_name |
|
| 178 | +461 |
- }+ ), |
|
| 179 | -+ | ||
| 462 | +! |
-
+ var_name, |
|
| 180 | +463 |
- ## server+ ... |
|
| 181 | -203x - | +||
| 464 | +
- checkmate::assert_function(server)+ ) |
||
| 182 | -203x - | +||
| 465 | +! |
- server_formals <- names(formals(server))+ invisible(self) |
|
| 183 | -203x - | +||
| 466 | +
- if (!(+ }, |
||
| 184 | -203x - | +||
| 467 | +
- "id" %in% server_formals ||+ #' @description |
||
| 185 | -203x - | +||
| 468 | +
- all(c("input", "output", "session") %in% server_formals)
+ #' Remove an active filter variable of a dataset from the active filter variables panel. |
||
| 186 | +469 |
- )) {
+ #' |
|
| 187 | -2x - | +||
| 470 | +
- stop(+ #' @param dataset_name (character) The name of the dataset to remove the filter variable from. |
||
| 188 | -2x - | +||
| 471 | +
- "\nmodule() `server` argument requires a function with following arguments:",+ #' If `NULL`, all the filter variables will be removed. |
||
| 189 | -2x - | +||
| 472 | +
- "\n - id - `teal` will set proper `shiny` namespace for this module.",+ #' @param var_name (character) The name of the variable to remove from the filter panel. |
||
| 190 | -2x - | +||
| 473 | +
- "\n - input, output, session (not recommended) - then `shiny::callModule` will be used to call a module.",+ #' If `NULL`, all the filter variables of the dataset will be removed. |
||
| 191 | -2x - | +||
| 474 | +
- "\n\nFollowing arguments can be used optionaly:",+ #' |
||
| 192 | -2x - | +||
| 475 | +
- "\n - `data` - module will receive list of reactive (filtered) data specified in the `filters` argument",+ #' @return The `TealAppDriver` object invisibly. |
||
| 193 | -2x - | +||
| 476 | +
- "\n - `datasets` - module will receive `FilteredData`. See `help(teal.slice::FilteredData)`",+ remove_filter_var = function(dataset_name = NULL, var_name = NULL) {
|
||
| 194 | -2x - | +||
| 477 | +! |
- "\n - `reporter` - module will receive `Reporter`. See `help(teal.reporter::Reporter)`",+ checkmate::check_string(dataset_name, null.ok = TRUE) |
|
| 195 | -2x - | +||
| 478 | +! |
- "\n - `filter_panel_api` - module will receive `FilterPanelAPI`. (See [teal.slice::FilterPanelAPI]).",+ checkmate::check_string(var_name, null.ok = TRUE) |
|
| 196 | -2x - | +||
| 479 | +! |
- "\n - `...` server_args elements will be passed to the module named argument or to the `...`"+ if (is.null(dataset_name)) {
|
|
| 197 | -+ | ||
| 480 | +! |
- )+ remove_selector <- sprintf( |
|
| 198 | -+ | ||
| 481 | +! |
- }+ "#%s-active-remove_all_filters", |
|
| 199 | -201x - | +||
| 482 | +! |
- if ("datasets" %in% server_formals) {
+ self$active_filters_ns() |
|
| 200 | -2x - | +||
| 483 | +
- warning(+ ) |
||
| 201 | -2x - | +||
| 484 | +! |
- sprintf("Called from module(label = \"%s\", ...)\n ", label),
+ } else if (is.null(var_name)) {
|
|
| 202 | -2x - | +||
| 485 | +! |
- "`datasets` argument in the server is deprecated and will be removed in the next release. ",+ remove_selector <- sprintf( |
|
| 203 | -2x - | +||
| 486 | +! |
- "Please use `data` instead.",+ "#%s-active-%s-remove_filters", |
|
| 204 | -2x - | +||
| 487 | +! |
- call. = FALSE+ self$active_filters_ns(), |
|
| 205 | -+ | ||
| 488 | +! |
- )+ dataset_name |
|
| 206 | +489 |
- }+ ) |
|
| 207 | +490 |
-
+ } else {
|
|
| 208 | -+ | ||
| 491 | +! |
-
+ remove_selector <- sprintf( |
|
| 209 | -+ | ||
| 492 | +! |
- ## UI+ "#%s-active-%s-filter-%s_%s-remove", |
|
| 210 | -201x - | +||
| 493 | +! |
- checkmate::assert_function(ui)+ self$active_filters_ns(), |
|
| 211 | -201x - | +||
| 494 | +! |
- ui_formals <- names(formals(ui))+ dataset_name, |
|
| 212 | -201x - | +||
| 495 | +! |
- if (!"id" %in% ui_formals) {
+ dataset_name, |
|
| 213 | -1x - | +||
| 496 | +! |
- stop(+ var_name |
|
| 214 | -1x - | +||
| 497 | +
- "\nmodule() `ui` argument requires a function with following arguments:",+ ) |
||
| 215 | -1x - | +||
| 498 | +
- "\n - id - `teal` will set proper `shiny` namespace for this module.",+ } |
||
| 216 | -1x - | +||
| 499 | +! |
- "\n\nFollowing arguments can be used optionally:",+ self$click( |
|
| 217 | -1x - | +||
| 500 | +! |
- "\n - `...` ui_args elements will be passed to the module argument of the same name or to the `...`"+ selector = remove_selector |
|
| 218 | +501 |
- )+ )+ |
+ |
| 502 | +! | +
+ invisible(self) |
|
| 219 | +503 |
- }+ }, |
|
| 220 | -200x - | +||
| 504 | +
- if (any(c("data", "datasets") %in% ui_formals)) {
+ #' @description |
||
| 221 | -2x - | +||
| 505 | +
- stop(+ #' Set the active filter values for a variable of a dataset in the active filter variable panel. |
||
| 222 | -2x - | +||
| 506 | +
- sprintf("Called from module(label = \"%s\", ...)\n ", label),
+ #' |
||
| 223 | -2x - | +||
| 507 | +
- "UI with `data` or `datasets` argument is no longer accepted.\n ",+ #' @param dataset_name (character) The name of the dataset to set the filter value for. |
||
| 224 | -2x - | +||
| 508 | +
- "If some UI inputs depend on data, please move the logic to your server instead.\n ",+ #' @param var_name (character) The name of the variable to set the filter value for. |
||
| 225 | -2x - | +||
| 509 | +
- "Possible solutions are renderUI() or updateXyzInput() functions."+ #' @param input The value to set the filter to. |
||
| 226 | +510 |
- )+ #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$set_inputs` |
|
| 227 | +511 |
- }+ #' |
|
| 228 | +512 |
-
+ #' @return The `TealAppDriver` object invisibly. |
|
| 229 | +513 |
-
+ set_active_filter_selection = function(dataset_name, |
|
| 230 | +514 |
- ## `filters`+ var_name, |
|
| 231 | -198x - | +||
| 515 | +
- if (!missing(filters)) {
+ input, |
||
| 232 | -! | +||
| 516 | +
- datanames <- filters+ ...) {
|
||
| 233 | +517 | ! |
- msg <-+ checkmate::check_string(dataset_name) |
| 234 | +518 | ! |
- "The `filters` argument is deprecated and will be removed in the next release. Please use `datanames` instead."+ checkmate::check_string(var_name) |
| 235 | +519 | ! |
- warning(msg)+ checkmate::check_string(input) |
| 236 | +520 |
- }+ |
|
| 237 | -+ | ||
| 521 | +! |
-
+ input_id_prefix <- sprintf( |
|
| 238 | -+ | ||
| 522 | +! |
- ## `datanames` (also including deprecated `filters`)+ "%s-filters-%s-filter-%s_%s-inputs", |
|
| 239 | -+ | ||
| 523 | +! |
- # please note a race condition between datanames set when filters is not missing and data arg in server function+ self$active_filters_ns(), |
|
| 240 | -198x - | +||
| 524 | +! |
- if (!is.element("data", server_formals) && !is.null(datanames)) {
+ dataset_name, |
|
| 241 | -12x - | +||
| 525 | +! |
- message(sprintf("module \"%s\" server function takes no data so \"datanames\" will be ignored", label))
+ dataset_name, |
|
| 242 | -12x - | +||
| 526 | +! |
- datanames <- NULL+ var_name |
|
| 243 | +527 |
- }- |
- |
| 244 | -198x - | -
- checkmate::assert_character(datanames, min.len = 1, null.ok = TRUE, any.missing = FALSE)+ ) |
|
| 245 | +528 | ||
| 246 | +529 |
- ## `server_args`+ # Find the type of filter (based on filter panel) |
|
| 247 | -197x - | +||
| 530 | +! |
- checkmate::assert_list(server_args, null.ok = TRUE, names = "named")+ supported_suffix <- c("selection", "selection_manual")
|
|
| 248 | -195x - | +||
| 531 | +! |
- srv_extra_args <- setdiff(names(server_args), server_formals)+ slices_suffix <- supported_suffix[ |
|
| 249 | -195x - | +||
| 532 | +! |
- if (length(srv_extra_args) > 0 && !"..." %in% server_formals) {
+ match( |
|
| 250 | -1x - | +||
| 533 | +! |
- stop(+ TRUE, |
|
| 251 | -1x - | +||
| 534 | +! |
- "\nFollowing `server_args` elements have no equivalent in the formals of the server:\n",+ vapply( |
|
| 252 | -1x - | +||
| 535 | +! |
- paste(paste(" -", srv_extra_args), collapse = "\n"),
+ supported_suffix, |
|
| 253 | -1x - | +||
| 536 | +! |
- "\n\nUpdate the server arguments by including above or add `...`"+ function(suffix) {
+ |
+ |
| 537 | +! | +
+ !is.null(self$get_html(sprintf("#%s-%s", input_id_prefix, suffix)))
|
|
| 254 | +538 |
- )+ },+ |
+ |
| 539 | +! | +
+ logical(1) |
|
| 255 | +540 |
- }+ ) |
|
| 256 | +541 |
-
+ ) |
|
| 257 | +542 |
- ## `ui_args`+ ] |
|
| 258 | -194x - | +||
| 543 | +
- checkmate::assert_list(ui_args, null.ok = TRUE, names = "named")+ |
||
| 259 | -192x - | +||
| 544 | +
- ui_extra_args <- setdiff(names(ui_args), ui_formals)+ # Generate correct namespace |
||
| 260 | -192x - | +||
| 545 | +! |
- if (length(ui_extra_args) > 0 && !"..." %in% ui_formals) {
+ slices_input_id <- sprintf( |
|
| 261 | -1x - | +||
| 546 | +! |
- stop(+ "%s-filters-%s-filter-%s_%s-inputs-%s", |
|
| 262 | -1x - | +||
| 547 | +! |
- "\nFollowing `ui_args` elements have no equivalent in the formals of UI:\n",+ self$active_filters_ns(), |
|
| 263 | -1x - | +||
| 548 | +! |
- paste(paste(" -", ui_extra_args), collapse = "\n"),
+ dataset_name, |
|
| 264 | -1x - | +||
| 549 | +! |
- "\n\nUpdate the UI arguments by including above or add `...`"+ dataset_name, |
|
| 265 | -+ | ||
| 550 | +! |
- )+ var_name, |
|
| 266 | -+ | ||
| 551 | +! |
- }+ slices_suffix |
|
| 267 | +552 |
-
+ ) |
|
| 268 | +553 |
- ## `transformers`+ |
|
| 269 | -191x - | +||
| 554 | +! |
- if (inherits(transformers, "teal_transform_module")) {
+ if (identical(slices_suffix, "selection_manual")) {
|
|
| 270 | -1x - | +||
| 555 | +! |
- transformers <- list(transformers)+ checkmate::assert_numeric(input, len = 2) |
|
| 271 | +556 |
- }+ |
|
| 272 | -191x - | +||
| 557 | +! |
- checkmate::assert_list(transformers, types = "teal_transform_module")+ dots <- rlang::list2(...) |
|
| 273 | -191x - | +||
| 558 | +! |
- transformer_datanames <- unlist(lapply(transformers, attr, "datanames"))+ checkmate::assert_choice(dots$priority_, formals(self$set_inputs)[["priority_"]], null.ok = TRUE) |
|
| 274 | -191x - | +||
| 559 | +! |
- combined_datanames <- if (identical(datanames, "all")) {
+ checkmate::assert_flag(dots$wait_, null.ok = TRUE) |
|
| 275 | -142x - | +||
| 560 | +
- "all"+ |
||
| 276 | -+ | ||
| 561 | +! |
- } else {
+ self$run_js( |
|
| 277 | -49x - | +||
| 562 | +! |
- union(datanames, transformer_datanames)+ sprintf( |
|
| 278 | -+ | ||
| 563 | +! |
- }+ "Shiny.setInputValue('%s:sw.numericRange', [%f, %f], {priority: '%s'})",
|
|
| 279 | -+ | ||
| 564 | +! |
-
+ slices_input_id, |
|
| 280 | -191x - | +||
| 565 | +! |
- structure(+ input[[1]], |
|
| 281 | -191x - | +||
| 566 | +! |
- list(+ input[[2]], |
|
| 282 | -191x - | +||
| 567 | +! |
- label = label,+ priority_ = ifelse(is.null(dots$priority_), "input", dots$priority_) |
|
| 283 | -191x - | +||
| 568 | +
- server = server,+ ) |
||
| 284 | -191x - | +||
| 569 | +
- ui = ui,+ ) |
||
| 285 | -191x - | +||
| 570 | +
- datanames = combined_datanames,+ |
||
| 286 | -191x - | +||
| 571 | +! |
- server_args = server_args,+ if (isTRUE(dots$wait_) || is.null(dots$wait_)) {
|
|
| 287 | -191x - | +||
| 572 | +! |
- ui_args = ui_args,+ self$wait_for_idle( |
|
| 288 | -191x - | +||
| 573 | +! |
- transformers = transformers+ timeout = if (is.null(dots$timeout_)) rlang::missing_arg() else dots$timeout_ |
|
| 289 | +574 |
- ),+ ) |
|
| 290 | -191x - | +||
| 575 | +
- class = "teal_module"+ } |
||
| 291 | -+ | ||
| 576 | +! |
- )+ } else if (identical(slices_suffix, "selection")) {
|
|
| 292 | -+ | ||
| 577 | +! |
- }+ self$set_input( |
|
| 293 | -+ | ||
| 578 | +! |
-
+ slices_input_id, |
|
| 294 | -+ | ||
| 579 | +! |
- #' @rdname teal_modules+ input, |
|
| 295 | +580 |
- #' @export+ ... |
|
| 296 | +581 |
- #'+ ) |
|
| 297 | +582 |
- modules <- function(..., label = "root") {
+ } else {
|
|
| 298 | -131x - | +||
| 583 | +! |
- checkmate::assert_string(label)+ stop("Filter selection set not supported for this slice.")
|
|
| 299 | -129x - | +||
| 584 | +
- submodules <- list(...)+ } |
||
| 300 | -129x - | +||
| 585 | +
- if (any(vapply(submodules, is.character, FUN.VALUE = logical(1)))) {
+
|
||
| 301 | -2x - | +||
| 586 | +! |
- stop(+ invisible(self) |
|
| 302 | -2x - | +||
| 587 | +
- "The only character argument to modules() must be 'label' and it must be named, ",+ }, |
||
| 303 | -2x - | +||
| 588 | +
- "change modules('lab', ...) to modules(label = 'lab', ...)"
+ #' @description |
||
| 304 | +589 |
- )+ #' Extract `html` attribute (found by a `selector`). |
|
| 305 | +590 |
- }+ #' |
|
| 306 | +591 |
-
+ #' @param selector (`character(1)`) specifying the selector to be used to get the content of a specific node. |
|
| 307 | -127x - | +||
| 592 | +
- checkmate::assert_list(submodules, min.len = 1, any.missing = FALSE, types = c("teal_module", "teal_modules"))
+ #' @param attribute (`character(1)`) name of an attribute to retrieve from a node specified by `selector`. |
||
| 308 | +593 |
- # name them so we can more easily access the children+ #' |
|
| 309 | +594 |
- # beware however that the label of the submodules should not be changed as it must be kept synced+ #' @return The `character` vector. |
|
| 310 | -124x - | +||
| 595 | +
- labels <- vapply(submodules, function(submodule) submodule$label, character(1))+ get_attr = function(selector, attribute) {
|
||
| 311 | -124x - | +||
| 596 | +! |
- names(submodules) <- get_unique_labels(labels)+ rvest::html_attr( |
|
| 312 | -124x - | +||
| 597 | +! |
- structure(+ rvest::html_nodes(self$get_html_rvest("html"), selector),
|
|
| 313 | -124x - | +||
| 598 | +! |
- list(+ attribute |
|
| 314 | -124x - | +||
| 599 | +
- label = label,+ ) |
||
| 315 | -124x - | +||
| 600 | +
- children = submodules+ }, |
||
| 316 | +601 |
- ),+ #' @description |
|
| 317 | -124x - | +||
| 602 | +
- class = "teal_modules"+ #' Wrapper around `get_html` that passes the output directly to `rvest::read_html`. |
||
| 318 | +603 |
- )+ #' |
|
| 319 | +604 |
- }+ #' @param selector `(character(1))` passed to `get_html`. |
|
| 320 | +605 |
-
+ #' |
|
| 321 | +606 |
- # printing methods ----+ #' @return An XML document. |
|
| 322 | +607 |
-
+ get_html_rvest = function(selector) {
+ |
+ |
| 608 | +! | +
+ rvest::read_html(self$get_html(selector)) |
|
| 323 | +609 |
- #' @rdname teal_modules+ }, |
|
| 324 | +610 |
- #' @export+ #' Wrapper around `get_url()` method that opens the app in the browser. |
|
| 325 | +611 |
- format.teal_module <- function(x, indent = 0, ...) {
+ #' |
|
| 326 | -3x - | +||
| 612 | +
- paste0(paste(rep(" ", indent), collapse = ""), "+ ", x$label, "\n", collapse = "")
+ #' @return Nothing. Opens the underlying teal app in the browser. |
||
| 327 | +613 |
- }+ open_url = function() {
+ |
+ |
| 614 | +! | +
+ browseURL(self$get_url()) |
|
| 328 | +615 |
-
+ }, |
|
| 329 | +616 |
-
+ #' @description |
|
| 330 | +617 |
- #' @rdname teal_modules+ #' Waits until a specified input, output, or export value. |
|
| 331 | +618 |
- #' @export+ #' This function serves as a wrapper around the `wait_for_value` method, |
|
| 332 | +619 |
- print.teal_module <- function(x, ...) {
+ #' providing a more flexible interface for waiting on different types of values within the active module namespace. |
|
| 333 | -! | +||
| 620 | +
- cat(format(x, ...))+ #' @param input,output,export A name of an input, output, or export value. |
||
| 334 | -! | +||
| 621 | +
- invisible(x)+ #' Only one of these parameters may be used. |
||
| 335 | +622 |
- }+ #' @param ... Must be empty. Allows for parameter expansion. |
|
| 336 | +623 |
-
+ #' Parameter with additional value to passed in `wait_for_value`. |
|
| 337 | +624 |
-
+ wait_for_active_module_value = function(input = rlang::missing_arg(), |
|
| 338 | +625 |
- #' @rdname teal_modules+ output = rlang::missing_arg(), |
|
| 339 | +626 |
- #' @export+ export = rlang::missing_arg(), |
|
| 340 | +627 |
- format.teal_modules <- function(x, indent = 0, ...) {
+ ...) {
|
|
| 341 | -1x - | +||
| 628 | +! |
- paste(+ ns <- shiny::NS(self$active_module_ns()) |
|
| 342 | -1x - | +||
| 629 | +
- c(+ |
||
| 343 | -1x - | +||
| 630 | +! |
- paste0(rep(" ", indent), "+ ", x$label, "\n"),
+ if (!rlang::is_missing(input) && checkmate::test_string(input, min.chars = 1)) input <- ns(input) |
|
| 344 | -1x - | +||
| 631 | +! |
- unlist(lapply(x$children, format, indent = indent + 1, ...))+ if (!rlang::is_missing(output) && checkmate::test_string(output, min.chars = 1)) output <- ns(output)+ |
+ |
| 632 | +! | +
+ if (!rlang::is_missing(export) && checkmate::test_string(export, min.chars = 1)) export <- ns(export) |
|
| 345 | +633 |
- ),+ |
|
| 346 | -1x - | +||
| 634 | +! |
- collapse = ""+ self$wait_for_value( |
|
| 347 | -+ | ||
| 635 | +! |
- )+ input = input, |
|
| 348 | -+ | ||
| 636 | +! |
- }+ output = output, |
|
| 349 | -+ | ||
| 637 | +! |
-
+ export = export, |
|
| 350 | +638 |
- #' @param modules (`teal_module` or `teal_modules`)+ ... |
|
| 351 | +639 |
- #' @rdname teal_modules+ ) |
|
| 352 | +640 |
- #' @examples+ } |
|
| 353 | +641 |
- #' # change the module's datanames+ ), |
|
| 354 | +642 |
- #' set_datanames(module(datanames = "all"), "a")+ # private members ---- |
|
| 355 | +643 |
- #'+ private = list( |
|
| 356 | +644 |
- #' # change modules' datanames+ # private attributes ---- |
|
| 357 | +645 |
- #' set_datanames(+ data = NULL, |
|
| 358 | +646 |
- #' modules(+ modules = NULL, |
|
| 359 | +647 |
- #' module(datanames = "all"),+ filter = teal_slices(), |
|
| 360 | +648 |
- #' module(datanames = "a")+ ns = list( |
|
| 361 | +649 |
- #' ),+ module = character(0), |
|
| 362 | +650 |
- #' "b"+ filter_panel = character(0) |
|
| 363 | +651 |
- #' )+ ), |
|
| 364 | +652 |
- #' @export+ # private methods ---- |
|
| 365 | +653 |
- set_datanames <- function(modules, datanames) {
+ set_active_ns = function() {
|
|
| 366 | +654 | ! |
- checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"))
+ all_inputs <- self$get_values()$input |
| 367 | +655 | ! |
- if (inherits(modules, "teal_modules")) {
+ active_tab_inputs <- all_inputs[grepl("-active_tab$", names(all_inputs))]
+ |
+
| 656 | ++ | + | |
| 368 | +657 | ! |
- modules$children <- lapply(modules$children, set_datanames, datanames)+ tab_ns <- unlist(lapply(names(active_tab_inputs), function(name) {
|
| 369 | -+ | ||
| 658 | +! |
- } else {
+ gsub( |
|
| 370 | +659 | ! |
- if (identical(modules$datanames, "all")) {
+ pattern = "-active_tab$", |
| 371 | +660 | ! |
- modules$datanames <- datanames+ replacement = sprintf("-%s", active_tab_inputs[[name]]),
+ |
+
| 661 | +! | +
+ name |
|
| 372 | +662 |
- } else {
+ )+ |
+ |
| 663 | ++ |
+ })) |
|
| 373 | +664 | ! |
- warning(+ active_ns <- tab_ns[1] |
| 374 | +665 | ! |
- "Not possible to modify datanames of the module ", modules$label,+ if (length(tab_ns) > 1) {
|
| 375 | +666 | ! |
- ". set_datanames() can only change datanames if it was set to \"all\".",+ for (i in 2:length(tab_ns)) {
|
| 376 | +667 | ! |
- call. = FALSE+ next_ns <- tab_ns[i]+ |
+
| 668 | +! | +
+ if (grepl(pattern = active_ns, next_ns)) {
+ |
+ |
| 669 | +! | +
+ active_ns <- next_ns |
|
| 377 | +670 |
- )+ } |
|
| 378 | +671 |
- }+ } |
|
| 379 | +672 |
- }+ } |
|
| 380 | +673 | ! |
- modules+ private$ns$module <- sprintf("%s-%s", active_ns, "module")
|
| 381 | +674 |
- }+ |
|
| 382 | -+ | ||
| 675 | +! |
-
+ components <- c("filter_panel", "data_summary")
|
|
| 383 | -+ | ||
| 676 | +! |
- #' @rdname teal_modules+ for (component in components) {
|
|
| 384 | +677 |
- #' @export+ if ( |
|
| 385 | -+ | ||
| 678 | +! |
- print.teal_modules <- print.teal_module+ !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)))
|
|
| 386 | +680 |
-
+ ) {
+ |
+ |
| 681 | +! | +
+ private$ns[[component]] <- sprintf("%s-%s", active_ns, component)
|
|
| 387 | +682 |
-
+ } else {
+ |
+ |
| 683 | +! | +
+ private$ns[[component]] <- sprintf("%s-module_%s", active_ns, component)
|
|
| 388 | +684 |
- # utilities ----+ } |
|
| 389 | +685 |
- ## subset or modify modules ----+ } |
|
| 390 | +686 |
-
+ }, |
|
| 391 | +687 |
- #' Append a `teal_module` to `children` of a `teal_modules` object+ # @description |
|
| 392 | +688 |
- #' @keywords internal+ # Get the active filter values from the active filter selection of dataset from the filter panel. |
|
| 393 | +689 |
- #' @param modules (`teal_modules`)+ # |
|
| 394 | +690 |
- #' @param module (`teal_module`) object to be appended onto the children of `modules`+ # @param dataset_name (character) The name of the dataset to get the filter values from. |
|
| 395 | +691 |
- #' @return A `teal_modules` object with `module` appended.+ # @param var_name (character) The name of the variable to get the filter values from. |
|
| 396 | +692 |
- append_module <- function(modules, module) {
+ # |
|
| 397 | -8x - | +||
| 693 | +
- checkmate::assert_class(modules, "teal_modules")+ # @return The value of the active filter selection. |
||
| 398 | -6x - | +||
| 694 | +
- checkmate::assert_class(module, "teal_module")+ get_active_filter_selection = function(dataset_name, var_name) {
|
||
| 399 | -4x - | +||
| 695 | +! |
- modules$children <- c(modules$children, list(module))+ checkmate::check_string(dataset_name) |
|
| 400 | -4x - | +||
| 696 | +! |
- labels <- vapply(modules$children, function(submodule) submodule$label, character(1))+ checkmate::check_string(var_name) |
|
| 401 | -4x - | +||
| 697 | +! |
- names(modules$children) <- get_unique_labels(labels)+ input_id_prefix <- sprintf( |
|
| 402 | -4x - | +||
| 698 | +! |
- modules+ "%s-filters-%s-filter-%s_%s-inputs", |
|
| 403 | -+ | ||
| 699 | +! |
- }+ self$active_filters_ns(), |
|
| 404 | -+ | ||
| 700 | +! |
-
+ dataset_name, |
|
| 405 | -+ | ||
| 701 | +! |
- #' Extract/Remove module(s) of specific class+ dataset_name, |
|
| 406 | -+ | ||
| 702 | +! |
- #'+ var_name |
|
| 407 | +703 |
- #' Given a `teal_module` or a `teal_modules`, return the elements of the structure according to `class`.+ ) |
|
| 408 | +704 |
- #'+ |
|
| 409 | +705 |
- #' @param modules (`teal_modules`)+ # Find the type of filter (categorical or range) |
|
| 410 | -+ | ||
| 706 | +! |
- #' @param class The class name of `teal_module` to be extracted or dropped.+ supported_suffix <- c("selection", "selection_manual")
|
|
| 411 | -+ | ||
| 707 | +! |
- #' @keywords internal+ for (suffix in supported_suffix) {
|
|
| 412 | -+ | ||
| 708 | +! |
- #' @return+ if (!is.null(self$get_html(sprintf("#%s-%s", input_id_prefix, suffix)))) {
|
|
| 413 | -+ | ||
| 709 | +! |
- #' - For `extract_module`, a `teal_module` of class `class` or `teal_modules` containing modules of class `class`.+ return(self$get_value(input = sprintf("%s-%s", input_id_prefix, suffix)))
|
|
| 414 | +710 |
- #' - For `drop_module`, the opposite, which is all `teal_modules` of class other than `class`.+ } |
|
| 415 | +711 |
- #' @rdname module_management+ } |
|
| 416 | +712 |
- extract_module <- function(modules, class) {
- |
- |
| 417 | -22x - | -
- if (inherits(modules, class)) {
+
|
|
| 418 | +713 | ! |
- modules+ NULL # If there are not any supported filters |
| 419 | -22x - | +||
| 714 | +
- } else if (inherits(modules, "teal_module")) {
+ }, |
||
| 420 | -12x - | +||
| 715 | +
- NULL+ # @description |
||
| 421 | -10x - | +||
| 716 | +
- } else if (inherits(modules, "teal_modules")) {
+ # Check if the page is stable without any `DOM` updates in the body of the app. |
||
| 422 | -10x - | +||
| 717 | +
- Filter(function(x) length(x) > 0L, lapply(modules$children, extract_module, class))+ # This is achieved by blocing the R process by sleeping until the page is unchanged till the `stability_period`. |
||
| 423 | +718 |
- }+ # @param stability_period (`numeric(1)`) The time in milliseconds to wait till the page to be stable. |
|
| 424 | +719 |
- }+ # @param check_interval (`numeric(1)`) The time in milliseconds to check for changes in the page. |
|
| 425 | +720 |
-
+ # The stability check is reset when a change is detected in the page after sleeping for check_interval. |
|
| 426 | +721 |
- #' @keywords internal+ wait_for_page_stability = function(stability_period = 2000, check_interval = 200) {
|
|
| 427 | -+ | ||
| 722 | +! |
- #' @return `teal_modules`+ previous_content <- self$get_html("body")
|
|
| 428 | -+ | ||
| 723 | +! |
- #' @rdname module_management+ end_time <- Sys.time() + (stability_period / 1000) |
|
| 429 | +724 |
- drop_module <- function(modules, class) {
+
|
|
| 430 | +725 | ! |
- if (inherits(modules, class)) {
+ repeat {
|
| 431 | +726 | ! |
- NULL+ Sys.sleep(check_interval / 1000) |
| 432 | +727 | ! |
- } else if (inherits(modules, "teal_module")) {
+ current_content <- self$get_html("body")
+ |
+
| 728 | ++ | + | |
| 433 | +729 | ! |
- modules+ if (!identical(previous_content, current_content)) {
|
| 434 | +730 | ! |
- } else if (inherits(modules, "teal_modules")) {
+ previous_content <- current_content |
| 435 | +731 | ! |
- do.call(+ end_time <- Sys.time() + (stability_period / 1000) |
| 436 | +732 | ! |
- "modules",+ } else if (Sys.time() >= end_time) {
|
| 437 | +733 | ! |
- c(Filter(function(x) length(x) > 0L, lapply(modules$children, drop_module, class)), label = modules$label)+ break |
| 438 | +734 |
- )+ } |
|
| 439 | +735 |
- }+ } |
|
| 440 | +736 |
- }+ } |
|
| 441 | +737 |
-
+ ) |
|
| 442 | +738 |
- ## read modules ----+ ) |
| 443 | +1 |
-
+ setOldClass("teal_module")
|
|
| 444 | +2 |
- #' Does the object make use of the `arg`+ setOldClass("teal_modules")
|
|
| 445 | +3 |
- #'+ |
|
| 446 | +4 |
- #' @param modules (`teal_module` or `teal_modules`) object+ #' Create `teal_module` and `teal_modules` objects |
|
| 447 | +5 |
- #' @param arg (`character(1)`) names of the arguments to be checked against formals of `teal` modules.+ #' |
|
| 448 | +6 |
- #' @return `logical` whether the object makes use of `arg`.+ #' @description |
|
| 449 | +7 |
- #' @rdname is_arg_used+ #' `r lifecycle::badge("stable")`
|
|
| 450 | +8 |
- #' @keywords internal+ #' Create a nested tab structure to embed modules in a `teal` application. |
|
| 451 | +9 |
- is_arg_used <- function(modules, arg) {
- |
- |
| 452 | -457x - | -
- checkmate::assert_string(arg)+ #' |
|
| 453 | -454x - | +||
| 10 | +
- if (inherits(modules, "teal_modules")) {
+ #' @details |
||
| 454 | -17x - | +||
| 11 | +
- any(unlist(lapply(modules$children, is_arg_used, arg)))+ #' `module()` creates an instance of a `teal_module` that can be placed in a `teal` application. |
||
| 455 | -437x - | +||
| 12 | +
- } else if (inherits(modules, "teal_module")) {
+ #' `modules()` shapes the structure of a the application by organizing `teal_module` within the navigation panel. |
||
| 456 | -29x - | +||
| 13 | +
- is_arg_used(modules$server, arg) || is_arg_used(modules$ui, arg)+ #' It wraps `teal_module` and `teal_modules` objects in a `teal_modules` object, |
||
| 457 | -408x - | +||
| 14 | +
- } else if (is.function(modules)) {
+ #' which results in a nested structure corresponding to the nested tabs in the final application. |
||
| 458 | -406x - | +||
| 15 | +
- isTRUE(arg %in% names(formals(modules)))+ #' |
||
| 459 | +16 |
- } else {
+ #' Note that for `modules()` `label` comes after `...`, so it must be passed as a named argument, |
|
| 460 | -2x - | +||
| 17 | +
- stop("is_arg_used function not implemented for this object")
+ #' otherwise it will be captured by `...`. |
||
| 461 | +18 |
- }+ #' |
|
| 462 | +19 |
- }+ #' The labels `"global_filters"` and `"Report previewer"` are reserved |
|
| 463 | +20 |
-
+ #' because they are used by the `mapping` argument of [teal_slices()] |
|
| 464 | +21 |
-
+ #' and the report previewer module [reporter_previewer_module()], respectively. |
|
| 465 | +22 |
- #' Get module depth+ #' |
|
| 466 | +23 |
- #'+ #' # Restricting datasets used by `teal_module`: |
|
| 467 | +24 |
- #' Depth starts at 0, so a single `teal.module` has depth 0.+ #' The `datanames` argument controls which datasets are used by the module’s server. These datasets, |
|
| 468 | +25 |
- #' Nesting it increases overall depth by 1.+ #' passed via server's `data` argument, are the only ones shown in the module's tab. |
|
| 469 | +26 |
#' |
|
| 470 | +27 |
- #' @inheritParams init+ #' When `datanames` is set to `"all"`, all datasets in the data object are treated as relevant. |
|
| 471 | +28 |
- #' @param depth optional integer determining current depth level+ #' However, this may include unnecessary datasets, such as: |
|
| 472 | +29 |
- #'+ #' - Proxy variables for column modifications |
|
| 473 | +30 |
- #' @return Depth level for given module.+ #' - Temporary datasets used to create final versions |
|
| 474 | +31 |
- #' @keywords internal+ #' - Connection objects |
|
| 475 | +32 |
- modules_depth <- function(modules, depth = 0L) {
+ #' |
|
| 476 | -12x - | +||
| 33 | +
- checkmate::assert_multi_class(modules, c("teal_module", "teal_modules"))
+ #' To exclude irrelevant datasets, use the [set_datanames()] function to change `datanames` from |
||
| 477 | -12x - | +||
| 34 | +
- checkmate::assert_int(depth, lower = 0)+ #' `"all"` to specific names. Trying to modify non-`"all"` values with [set_datanames()] will result |
||
| 478 | -11x - | +||
| 35 | +
- if (inherits(modules, "teal_modules")) {
+ #' in a warning. Datasets with names starting with . are ignored globally unless explicitly listed |
||
| 479 | -4x - | +||
| 36 | +
- max(vapply(modules$children, modules_depth, integer(1), depth = depth + 1L))+ #' in `datanames`. |
||
| 480 | +37 |
- } else {
+ #' |
|
| 481 | -7x - | +||
| 38 | +
- depth+ #' # `datanames` with `transformers` |
||
| 482 | +39 |
- }+ #' When transformers are specified, their `datanames` are added to the module’s `datanames`, which |
|
| 483 | +40 |
- }+ #' changes the behavior as follows: |
|
| 484 | +41 |
-
+ #' - If `module(datanames)` is `NULL` and the `transformers` have defined `datanames`, the sidebar |
|
| 485 | +42 |
- #' Retrieve labels from `teal_modules`+ #' will appear showing the `transformers`' datasets, instead of being hidden. |
|
| 486 | +43 |
- #'+ #' - If `module(datanames)` is set to specific values and any `transformer` has `datanames = "all"`, |
|
| 487 | +44 |
- #' @param modules (`teal_modules`)+ #' the module may receive extra datasets that could be unnecessary |
|
| 488 | +45 |
- #' @return A `list` containing the labels of the modules. If the modules are nested,+ #' |
|
| 489 | +46 |
- #' the function returns a nested `list` of labels.+ #' @param label (`character(1)`) Label shown in the navigation item for the module or module group. |
|
| 490 | +47 |
- #' @keywords internal+ #' For `modules()` defaults to `"root"`. See `Details`. |
|
| 491 | +48 |
- module_labels <- function(modules) {
+ #' @param server (`function`) `shiny` module with following arguments: |
|
| 492 | -179x - | +||
| 49 | +
- if (inherits(modules, "teal_modules")) {
+ #' - `id` - `teal` will set proper `shiny` namespace for this module (see [shiny::moduleServer()]). |
||
| 493 | -77x - | +||
| 50 | +
- lapply(modules$children, module_labels)+ #' - `input`, `output`, `session` - (optional; not recommended) When provided, then [shiny::callModule()] |
||
| 494 | +51 |
- } else {
+ #' will be used to call a module. From `shiny` 1.5.0, the recommended way is to use |
|
| 495 | -102x - | +||
| 52 | +
- modules$label+ #' [shiny::moduleServer()] instead which doesn't require these arguments. |
||
| 496 | +53 |
- }+ #' - `data` (optional) When provided, the module will be called with `teal_data` object (i.e. a list of |
|
| 497 | +54 |
- }+ #' reactive (filtered) data specified in the `filters` argument) as the value of this argument. |
|
| 498 | +55 |
-
+ #' - `datasets` (optional) When provided, the module will be called with `FilteredData` object as the |
|
| 499 | +56 |
- #' Retrieve `teal_bookmarkable` attribute from `teal_modules`+ #' value of this argument. (See [`teal.slice::FilteredData`]). |
|
| 500 | +57 |
- #'+ #' - `reporter` (optional) When provided, the module will be called with `Reporter` object as the value |
|
| 501 | +58 |
- #' @param modules (`teal_modules` or `teal_module`) object+ #' of this argument. (See [`teal.reporter::Reporter`]). |
|
| 502 | +59 |
- #' @return named list of the same structure as `modules` with `TRUE` or `FALSE` values indicating+ #' - `filter_panel_api` (optional) When provided, the module will be called with `FilterPanelAPI` object |
|
| 503 | +60 |
- #' whether the module is bookmarkable.+ #' as the value of this argument. (See [`teal.slice::FilterPanelAPI`]). |
|
| 504 | +61 |
- #' @keywords internal+ #' - `...` (optional) When provided, `server_args` elements will be passed to the module named argument |
|
| 505 | +62 |
- modules_bookmarkable <- function(modules) {
+ #' or to the `...`. |
|
| 506 | -179x - | +||
| 63 | +
- checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"))
+ #' @param ui (`function`) `shiny` UI module function with following arguments: |
||
| 507 | -179x - | +||
| 64 | +
- if (inherits(modules, "teal_modules")) {
+ #' - `id` - `teal` will set proper `shiny` namespace for this module. |
||
| 508 | -77x - | +||
| 65 | +
- setNames(+ #' - `...` (optional) When provided, `ui_args` elements will be passed to the module named argument |
||
| 509 | -77x - | +||
| 66 | +
- lapply(modules$children, modules_bookmarkable),+ #' or to the `...`. |
||
| 510 | -77x - | +||
| 67 | +
- vapply(modules$children, `[[`, "label", FUN.VALUE = character(1))+ #' @param filters (`character`) Deprecated. Use `datanames` instead. |
||
| 511 | +68 |
- )+ #' @param datanames (`character`) Names of the datasets relevant to the item. |
|
| 512 | +69 |
- } else {
+ #' There are 2 reserved values that have specific behaviors: |
|
| 513 | -102x - | +||
| 70 | +
- attr(modules, "teal_bookmarkable", exact = TRUE)+ #' - The keyword `"all"` includes all datasets available in the data passed to the teal application. |
||
| 514 | +71 |
- }+ #' - `NULL` hides the sidebar panel completely. |
|
| 515 | +72 |
- }+ #' - If `transformers` are specified, their `datanames` are automatically added to this `datanames` |
| 1 | +73 |
- #' Landing popup module+ #' argument. |
|
| 2 | +74 |
- #'+ #' @param server_args (named `list`) with additional arguments passed on to the server function. |
|
| 3 | +75 |
- #' @description Creates a landing welcome popup for `teal` applications.+ #' @param ui_args (named `list`) with additional arguments passed on to the UI function. |
|
| 4 | +76 |
- #'+ #' @param x (`teal_module` or `teal_modules`) Object to format/print. |
|
| 5 | +77 |
- #' This module is used to display a popup dialog when the application starts.+ #' @param indent (`integer(1)`) Indention level; each nested element is indented one level more. |
|
| 6 | +78 |
- #' The dialog blocks access to the application and must be closed with a button before the application can be viewed.+ #' @param transformers (`list` of `teal_data_module`) that will be applied to transform the data. |
|
| 7 | +79 |
- #'+ #' Each transform module UI will appear in the `teal`'s sidebar panel. |
|
| 8 | +80 |
- #' @param label (`character(1)`) Label of the module.+ #' Transformers' `datanames` are added to the `datanames`. See [teal_transform_module()]. |
|
| 9 | +81 |
- #' @param title (`character(1)`) Text to be displayed as popup title.+ #' |
|
| 10 | +82 |
- #' @param content (`character(1)`, `shiny.tag` or `shiny.tag.list`) with the content of the popup.+ #' @param ... |
|
| 11 | +83 |
- #' Passed to `...` of `shiny::modalDialog`. See examples.+ #' - For `modules()`: (`teal_module` or `teal_modules`) Objects to wrap into a tab. |
|
| 12 | +84 |
- #' @param buttons (`shiny.tag` or `shiny.tag.list`) Typically a `modalButton` or `actionButton`. See examples.+ #' - For `format()` and `print()`: Arguments passed to other methods. |
|
| 13 | +85 |
#' |
|
| 14 | +86 |
- #' @return A `teal_module` (extended with `teal_landing_module` class) to be used in `teal` applications.+ #' @return |
|
| 15 | +87 |
- #'+ #' `module()` returns an object of class `teal_module`. |
|
| 16 | +88 |
- #' @examples+ #' |
|
| 17 | +89 |
- #' app1 <- init(+ #' `modules()` returns a `teal_modules` object which contains following fields: |
|
| 18 | +90 |
- #' data = teal_data(iris = iris),+ #' - `label`: taken from the `label` argument. |
|
| 19 | +91 |
- #' modules = modules(+ #' - `children`: a list containing objects passed in `...`. List elements are named after |
|
| 20 | +92 |
- #' example_module()+ #' their `label` attribute converted to a valid `shiny` id. |
|
| 21 | +93 |
- #' ),+ #' |
|
| 22 | +94 |
- #' landing_popup = landing_popup_module(+ #' @name teal_modules |
|
| 23 | +95 |
- #' content = "A place for the welcome message or a disclaimer statement.",+ #' @aliases teal_module |
|
| 24 | +96 |
- #' buttons = modalButton("Proceed")
+ #' |
|
| 25 | +97 |
- #' )+ #' @examples |
|
| 26 | +98 |
- #' )+ #' library(shiny) |
|
| 27 | +99 |
- #' if (interactive()) {
+ #' |
|
| 28 | +100 |
- #' shinyApp(app1$ui, app1$server)+ #' module_1 <- module( |
|
| 29 | +101 |
- #' }+ #' label = "a module", |
|
| 30 | +102 |
- #'+ #' server = function(id, data) {
|
|
| 31 | +103 |
- #' app2 <- init(+ #' moduleServer( |
|
| 32 | +104 |
- #' data = teal_data(iris = iris),+ #' id, |
|
| 33 | +105 |
- #' modules = modules(+ #' module = function(input, output, session) {
|
|
| 34 | +106 |
- #' example_module()+ #' output$data <- renderDataTable(data()[["iris"]]) |
|
| 35 | +107 |
- #' ),+ #' } |
|
| 36 | +108 |
- #' landing_popup = landing_popup_module(+ #' ) |
|
| 37 | +109 |
- #' title = "Welcome",+ #' }, |
|
| 38 | +110 |
- #' content = tags$b(+ #' ui = function(id) {
|
|
| 39 | +111 |
- #' "A place for the welcome message or a disclaimer statement.",+ #' ns <- NS(id) |
|
| 40 | +112 |
- #' style = "color: red;"+ #' tagList(dataTableOutput(ns("data")))
|
|
| 41 | +113 |
- #' ),+ #' }, |
|
| 42 | +114 |
- #' buttons = tagList(+ #' datanames = "all" |
|
| 43 | +115 |
- #' modalButton("Proceed"),
+ #' ) |
|
| 44 | +116 |
- #' actionButton("read", "Read more",
+ #' |
|
| 45 | +117 |
- #' onclick = "window.open('http://google.com', '_blank')"
+ #' module_2 <- module( |
|
| 46 | +118 |
- #' ),+ #' label = "another module", |
|
| 47 | +119 |
- #' actionButton("close", "Reject", onclick = "window.close()")
+ #' server = function(id) {
|
|
| 48 | +120 |
- #' )+ #' moduleServer( |
|
| 49 | +121 |
- #' )+ #' id, |
|
| 50 | +122 |
- #' )+ #' module = function(input, output, session) {
|
|
| 51 | +123 |
- #'+ #' output$text <- renderText("Another Module")
|
|
| 52 | +124 |
- #' if (interactive()) {
+ #' } |
|
| 53 | +125 |
- #' shinyApp(app2$ui, app2$server)+ #' ) |
|
| 54 | +126 |
- #' }+ #' }, |
|
| 55 | +127 |
- #'+ #' ui = function(id) {
|
|
| 56 | +128 |
- #' @export+ #' ns <- NS(id) |
|
| 57 | +129 |
- landing_popup_module <- function(label = "Landing Popup",+ #' tagList(textOutput(ns("text")))
|
|
| 58 | +130 |
- title = NULL,+ #' }, |
|
| 59 | +131 |
- content = NULL,+ #' datanames = NULL |
|
| 60 | +132 |
- buttons = modalButton("Accept")) {
- |
- |
| 61 | -! | -
- checkmate::assert_string(label)- |
- |
| 62 | -! | -
- checkmate::assert_string(title, null.ok = TRUE)- |
- |
| 63 | -! | -
- checkmate::assert_multi_class(- |
- |
| 64 | -! | -
- content,- |
- |
| 65 | -! | -
- classes = c("character", "shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE
+ #' ) |
|
| 66 | +133 |
- )- |
- |
| 67 | -! | -
- checkmate::assert_multi_class(buttons, classes = c("shiny.tag", "shiny.tag.list"))
+ #' |
|
| 68 | +134 | - - | -|
| 69 | -! | -
- message("Initializing landing_popup_module")
+ #' modules <- modules( |
|
| 70 | +135 | - - | -|
| 71 | -! | -
- module <- module(- |
- |
| 72 | -! | -
- label = label,- |
- |
| 73 | -! | -
- server = function(id) {
- |
- |
| 74 | -! | -
- moduleServer(id, function(input, output, session) {
- |
- |
| 75 | -! | -
- showModal(- |
- |
| 76 | -! | -
- modalDialog(- |
- |
| 77 | -! | -
- id = "landingpopup",- |
- |
| 78 | -! | -
- title = title,- |
- |
| 79 | -! | -
- content,- |
- |
| 80 | -! | -
- footer = buttons+ #' label = "modules", |
|
| 81 | +136 |
- )+ #' modules( |
|
| 82 | +137 |
- )+ #' label = "nested modules", |
|
| 83 | +138 |
- })+ #' module_1 |
|
| 84 | +139 |
- }+ #' ), |
|
| 85 | +140 |
- )- |
- |
| 86 | -! | -
- class(module) <- c("teal_module_landing", class(module))
- |
- |
| 87 | -! | -
- module+ #' module_2 |
|
| 88 | +141 |
- }+ #' ) |
| 1 | +142 |
- #' Manage multiple `FilteredData` objects+ #' |
||
| 2 | +143 |
- #'+ #' app <- init( |
||
| 3 | +144 |
- #' @description+ #' data = teal_data(iris = iris), |
||
| 4 | +145 |
- #' Oversee filter states across the entire application.+ #' modules = modules |
||
| 5 | +146 |
- #'+ #' ) |
||
| 6 | +147 |
- #' @section Slices global:+ #' |
||
| 7 | +148 |
- #' The key role in maintaining the module-specific filter states is played by the `.slicesGlobal`+ #' if (interactive()) {
|
||
| 8 | +149 |
- #' object. It is a reference class that holds the following fields:+ #' shinyApp(app$ui, app$server) |
||
| 9 | +150 |
- #' - `all_slices` (`reactiveVal`) - reactive value containing all filters registered in an app.+ #' } |
||
| 10 | +151 |
- #' - `module_slices_api` (`reactiveValues`) - reactive field containing references to each modules'+ #' @rdname teal_modules |
||
| 11 | +152 |
- #' `FilteredData` object methods. At this moment it is used only in `srv_filter_manager` to display+ #' @export |
||
| 12 | +153 |
- #' the filter states in a table combining informations from `all_slices` and from+ #' |
||
| 13 | +154 |
- #' `FilteredData$get_available_teal_slices()`.+ module <- function(label = "module", |
||
| 14 | +155 |
- #'+ server = function(id, data, ...) moduleServer(id, function(input, output, session) NULL), |
||
| 15 | +156 |
- #' During a session only new filters are added to `all_slices` unless [`module_snapshot_manager`] is+ ui = function(id, ...) tags$p(paste0("This module has no UI (id: ", id, " )")),
|
||
| 16 | +157 |
- #' used to restore previous state. Filters from `all_slices` can be activated or deactivated in a+ filters, |
||
| 17 | +158 |
- #' module which is linked (both ways) by `attr(, "mapping")` so that:+ datanames = "all", |
||
| 18 | +159 |
- #' - If module's filter is added or removed in its `FilteredData` object, this information is passed+ server_args = NULL, |
||
| 19 | +160 |
- #' to `SlicesGlobal` which updates `attr(, "mapping")` accordingly.+ ui_args = NULL, |
||
| 20 | +161 |
- #' - When mapping changes in a `SlicesGlobal`, filters are set or removed from module's+ transformers = list()) {
|
||
| 21 | +162 |
- #' `FilteredData`.+ # argument checking (independent) |
||
| 22 | +163 |
- #'+ ## `label` |
||
| 23 | -+ | |||
| 164 | +211x |
- #' @section Filter manager:+ checkmate::assert_string(label) |
||
| 24 | -+ | |||
| 165 | +208x |
- #' Filter-manager is split into two parts:+ if (label == "global_filters") {
|
||
| 25 | -+ | |||
| 166 | +1x |
- #' 1. `ui/srv_filter_manager_panel` - Called once for the whole app. This module observes changes in+ stop( |
||
| 26 | -+ | |||
| 167 | +1x |
- #' the filters in `slices_global` and displays them in a table utilizing information from `mapping`:+ sprintf("module(label = \"%s\", ...\n ", label),
|
||
| 27 | -+ | |||
| 168 | +1x |
- #' - (`TRUE`) - filter is active in the module+ "Label 'global_filters' is reserved in teal. Please change to something else.", |
||
| 28 | -+ | |||
| 169 | +1x |
- #' - (`FALSE`) - filter is inactive in the module+ call. = FALSE |
||
| 29 | +170 |
- #' - (`NA`) - filter is not available in the module+ ) |
||
| 30 | +171 |
- #' 2. `ui/srv_module_filter_manager` - Called once for each `teal_module`. Handling filter states+ } |
||
| 31 | -+ | |||
| 172 | +207x |
- #' for of single module and keeping module `FilteredData` consistent with `slices_global`, so that+ if (label == "Report previewer") {
|
||
| 32 | -+ | |||
| 173 | +! |
- #' local filters are always reflected in the `slices_global` and its mapping and vice versa.+ stop( |
||
| 33 | -+ | |||
| 174 | +! |
- #'+ sprintf("module(label = \"%s\", ...\n ", label),
|
||
| 34 | -+ | |||
| 175 | +! |
- #'+ "Label 'Report previewer' is reserved in teal. Please change to something else.", |
||
| 35 | -+ | |||
| 176 | +! |
- #' @param id (`character(1)`)+ call. = FALSE |
||
| 36 | +177 |
- #' `shiny` module instance id.+ ) |
||
| 37 | +178 |
- #'+ } |
||
| 38 | +179 |
- #' @param slices_global (`reactiveVal`)+ |
||
| 39 | +180 |
- #' containing `teal_slices`.+ ## server |
||
| 40 | -+ | |||
| 181 | +207x |
- #'+ checkmate::assert_function(server) |
||
| 41 | -+ | |||
| 182 | +207x |
- #' @param module_fd (`FilteredData`)+ server_formals <- names(formals(server)) |
||
| 42 | -+ | |||
| 183 | +207x |
- #' Object containing the data to be filtered in a single `teal` module.+ if (!( |
||
| 43 | -+ | |||
| 184 | +207x |
- #'+ "id" %in% server_formals || |
||
| 44 | -+ | |||
| 185 | +207x |
- #' @return+ all(c("input", "output", "session") %in% server_formals)
|
||
| 45 | +186 |
- #' Module returns a `slices_global` (`reactiveVal`) containing a `teal_slices` object with mapping.+ )) {
|
||
| 46 | -+ | |||
| 187 | +2x |
- #'+ stop( |
||
| 47 | -+ | |||
| 188 | +2x |
- #' @encoding UTF-8+ "\nmodule() `server` argument requires a function with following arguments:", |
||
| 48 | -+ | |||
| 189 | +2x |
- #'+ "\n - id - `teal` will set proper `shiny` namespace for this module.", |
||
| 49 | -+ | |||
| 190 | +2x |
- #' @name module_filter_manager+ "\n - input, output, session (not recommended) - then `shiny::callModule` will be used to call a module.", |
||
| 50 | -+ | |||
| 191 | +2x |
- #' @rdname module_filter_manager+ "\n\nFollowing arguments can be used optionaly:", |
||
| 51 | -+ | |||
| 192 | +2x |
- #'+ "\n - `data` - module will receive list of reactive (filtered) data specified in the `filters` argument", |
||
| 52 | -+ | |||
| 193 | +2x |
- NULL+ "\n - `datasets` - module will receive `FilteredData`. See `help(teal.slice::FilteredData)`", |
||
| 53 | -+ | |||
| 194 | +2x |
-
+ "\n - `reporter` - module will receive `Reporter`. See `help(teal.reporter::Reporter)`", |
||
| 54 | -+ | |||
| 195 | +2x |
- #' @rdname module_filter_manager+ "\n - `filter_panel_api` - module will receive `FilterPanelAPI`. (See [teal.slice::FilterPanelAPI]).",+ |
+ ||
| 196 | +2x | +
+ "\n - `...` server_args elements will be passed to the module named argument or to the `...`" |
||
| 55 | +197 |
- ui_filter_manager_panel <- function(id) {
+ ) |
||
| 56 | -! | +|||
| 198 | +
- ns <- NS(id)+ } |
|||
| 57 | -! | +|||
| 199 | +205x |
- tags$button(+ if ("datasets" %in% server_formals) {
|
||
| 58 | -! | +|||
| 200 | +2x |
- id = ns("show_filter_manager"),
+ warning( |
||
| 59 | -! | +|||
| 201 | +2x |
- class = "btn action-button wunder_bar_button",+ sprintf("Called from module(label = \"%s\", ...)\n ", label),
|
||
| 60 | -! | +|||
| 202 | +2x |
- title = "View filter mapping",+ "`datasets` argument in the server is deprecated and will be removed in the next release. ", |
||
| 61 | -! | +|||
| 203 | +2x |
- suppressMessages(icon("fas fa-grip"))
+ "Please use `data` instead.", |
||
| 62 | -+ | |||
| 204 | +2x |
- )+ call. = FALSE |
||
| 63 | +205 |
- }+ ) |
||
| 64 | +206 |
-
+ } |
||
| 65 | +207 |
- #' @rdname module_filter_manager+ |
||
| 66 | +208 |
- #' @keywords internal+ |
||
| 67 | +209 |
- srv_filter_manager_panel <- function(id, slices_global) {
+ ## UI |
||
| 68 | -77x - | +210 | +205x |
- checkmate::assert_string(id)+ checkmate::assert_function(ui) |
| 69 | -77x - | +211 | +205x |
- checkmate::assert_class(slices_global, ".slicesGlobal")+ ui_formals <- names(formals(ui)) |
| 70 | -77x - | +212 | +205x |
- moduleServer(id, function(input, output, session) {
+ if (!"id" %in% ui_formals) {
|
| 71 | -77x - | +213 | +1x |
- setBookmarkExclude(c("show_filter_manager"))
+ stop( |
| 72 | -77x - | -
- observeEvent(input$show_filter_manager, {
- |
- ||
| 73 | -! | +214 | +1x |
- logger::log_debug("srv_filter_manager_panel@1 show_filter_manager button has been clicked.")
+ "\nmodule() `ui` argument requires a function with following arguments:", |
| 74 | -! | +|||
| 215 | +1x |
- showModal(+ "\n - id - `teal` will set proper `shiny` namespace for this module.", |
||
| 75 | -! | +|||
| 216 | +1x |
- modalDialog(+ "\n\nFollowing arguments can be used optionally:", |
||
| 76 | -! | +|||
| 217 | +1x |
- ui_filter_manager(session$ns("filter_manager")),
+ "\n - `...` ui_args elements will be passed to the module argument of the same name or to the `...`" |
||
| 77 | -! | +|||
| 218 | +
- class = "filter_manager_modal",+ ) |
|||
| 78 | -! | +|||
| 219 | +
- size = "l",+ } |
|||
| 79 | -! | +|||
| 220 | +204x |
- footer = NULL,+ if (any(c("data", "datasets") %in% ui_formals)) {
|
||
| 80 | -! | +|||
| 221 | +2x |
- easyClose = TRUE+ stop( |
||
| 81 | -+ | |||
| 222 | +2x |
- )+ sprintf("Called from module(label = \"%s\", ...)\n ", label),
|
||
| 82 | -+ | |||
| 223 | +2x |
- )+ "UI with `data` or `datasets` argument is no longer accepted.\n ", |
||
| 83 | -+ | |||
| 224 | +2x |
- })+ "If some UI inputs depend on data, please move the logic to your server instead.\n ", |
||
| 84 | -77x - | +225 | +2x |
- srv_filter_manager("filter_manager", slices_global = slices_global)
+ "Possible solutions are renderUI() or updateXyzInput() functions." |
| 85 | +226 |
- })+ ) |
||
| 86 | +227 |
- }+ } |
||
| 87 | +228 | |||
| 88 | +229 |
- #' @rdname module_filter_manager+ |
||
| 89 | +230 |
- ui_filter_manager <- function(id) {
+ ## `filters` |
||
| 90 | -! | +|||
| 231 | +202x |
- ns <- NS(id)+ if (!missing(filters)) {
|
||
| 91 | +232 | ! |
- actionButton(ns("filter_manager"), NULL, icon = icon("fas fa-filter"))
+ datanames <- filters |
|
| 92 | +233 | ! |
- tags$div(+ msg <- |
|
| 93 | +234 | ! |
- class = "filter_manager_content",+ "The `filters` argument is deprecated and will be removed in the next release. Please use `datanames` instead." |
|
| 94 | +235 | ! |
- tableOutput(ns("slices_table"))
+ warning(msg) |
|
| 95 | +236 |
- )+ } |
||
| 96 | +237 |
- }+ |
||
| 97 | +238 |
-
+ ## `datanames` (also including deprecated `filters`) |
||
| 98 | +239 |
- #' @rdname module_filter_manager+ # please note a race condition between datanames set when filters is not missing and data arg in server function |
||
| 99 | -+ | |||
| 240 | +202x |
- srv_filter_manager <- function(id, slices_global) {
+ if (!is.element("data", server_formals) && !is.null(datanames)) {
|
||
| 100 | -77x - | +241 | +12x |
- checkmate::assert_string(id)+ message(sprintf("module \"%s\" server function takes no data so \"datanames\" will be ignored", label))
|
| 101 | -77x - | +242 | +12x |
- checkmate::assert_class(slices_global, ".slicesGlobal")+ datanames <- NULL |
| 102 | +243 | - - | -||
| 103 | -77x - | -
- moduleServer(id, function(input, output, session) {
+ } |
||
| 104 | -77x - | +244 | +202x |
- logger::log_debug("filter_manager_srv initializing.")
+ checkmate::assert_character(datanames, min.len = 1, null.ok = TRUE, any.missing = FALSE) |
| 105 | +245 | |||
| 106 | +246 |
- # Bookmark slices global with mapping.+ ## `server_args` |
||
| 107 | -77x - | +247 | +201x |
- session$onBookmark(function(state) {
+ checkmate::assert_list(server_args, null.ok = TRUE, names = "named") |
| 108 | -! | +|||
| 248 | +199x |
- logger::log_debug("filter_manager_srv@onBookmark: storing filter state")
+ srv_extra_args <- setdiff(names(server_args), server_formals) |
||
| 109 | -! | +|||
| 249 | +199x |
- state$values$filter_state_on_bookmark <- as.list(+ if (length(srv_extra_args) > 0 && !"..." %in% server_formals) {
|
||
| 110 | -! | +|||
| 250 | +1x |
- slices_global$all_slices(),+ stop( |
||
| 111 | -! | +|||
| 251 | +1x |
- recursive = TRUE+ "\nFollowing `server_args` elements have no equivalent in the formals of the server:\n",+ |
+ ||
| 252 | +1x | +
+ paste(paste(" -", srv_extra_args), collapse = "\n"),
+ |
+ ||
| 253 | +1x | +
+ "\n\nUpdate the server arguments by including above or add `...`" |
||
| 112 | +254 |
- )+ ) |
||
| 113 | +255 |
- })+ } |
||
| 114 | +256 | |||
| 257 | ++ |
+ ## `ui_args`+ |
+ ||
| 115 | -77x - | +258 | +198x |
- bookmarked_slices <- restoreValue(session$ns("filter_state_on_bookmark"), NULL)
+ checkmate::assert_list(ui_args, null.ok = TRUE, names = "named") |
| 116 | -77x - | +259 | +196x |
- if (!is.null(bookmarked_slices)) {
+ ui_extra_args <- setdiff(names(ui_args), ui_formals) |
| 117 | -! | +|||
| 260 | +196x |
- logger::log_debug("filter_manager_srv: restoring filter state from bookmark.")
+ if (length(ui_extra_args) > 0 && !"..." %in% ui_formals) {
|
||
| 118 | -! | +|||
| 261 | +1x |
- slices_global$slices_set(bookmarked_slices)+ stop( |
||
| 119 | -+ | |||
| 262 | +1x |
- }+ "\nFollowing `ui_args` elements have no equivalent in the formals of UI:\n", |
||
| 120 | -+ | |||
| 263 | +1x |
-
+ paste(paste(" -", ui_extra_args), collapse = "\n"),
|
||
| 121 | -77x - | +264 | +1x |
- mapping_table <- reactive({
+ "\n\nUpdate the UI arguments by including above or add `...`" |
| 122 | +265 |
- # We want this to be reactive on slices_global$all_slices() only as get_available_teal_slices()+ ) |
||
| 123 | +266 |
- # is dependent on slices_global$all_slices().+ } |
||
| 124 | -86x - | +|||
| 267 | +
- module_labels <- setdiff(+ + |
+ |||
| 268 | ++ |
+ ## `transformers` |
||
| 125 | -86x - | +269 | +195x |
- names(attr(slices_global$all_slices(), "mapping")),+ if (inherits(transformers, "teal_transform_module")) {
|
| 126 | -86x - | +270 | +1x |
- "Report previewer"+ transformers <- list(transformers) |
| 127 | +271 |
- )+ } |
||
| 128 | -86x - | +272 | +195x |
- isolate({
+ checkmate::assert_list(transformers, types = "teal_transform_module") |
| 129 | -86x - | +273 | +195x |
- mm <- as.data.frame(+ transformer_datanames <- unlist(lapply(transformers, attr, "datanames")) |
| 130 | -86x - | +274 | +195x |
- sapply(+ combined_datanames <- if (identical(datanames, "all")) {
|
| 131 | -86x - | +275 | +142x |
- module_labels,+ "all" |
| 132 | -86x - | +|||
| 276 | +
- simplify = FALSE,+ } else {
|
|||
| 133 | -86x - | +277 | +53x |
- function(module_label) {
+ union(datanames, transformer_datanames) |
| 134 | -99x - | +|||
| 278 | +
- available_slices <- slices_global$module_slices_api[[module_label]]$get_available_teal_slices()+ } |
|||
| 135 | -91x - | +|||
| 279 | +
- global_ids <- sapply(slices_global$all_slices(), `[[`, "id", simplify = FALSE)+ |
|||
| 136 | -91x - | +280 | +195x |
- module_ids <- sapply(slices_global$slices_get(module_label), `[[`, "id", simplify = FALSE)+ structure( |
| 137 | -91x - | +281 | +195x |
- allowed_ids <- vapply(available_slices, `[[`, character(1L), "id")+ list( |
| 138 | -91x - | +282 | +195x |
- active_ids <- global_ids %in% module_ids+ label = label, |
| 139 | -91x - | +283 | +195x |
- setNames(nm = global_ids, ifelse(global_ids %in% allowed_ids, active_ids, NA))+ server = server, |
| 140 | -+ | |||
| 284 | +195x |
- }+ ui = ui, |
||
| 141 | -+ | |||
| 285 | +195x |
- ),+ datanames = combined_datanames, |
||
| 142 | -86x - | +286 | +195x |
- check.names = FALSE+ server_args = server_args, |
| 143 | -+ | |||
| 287 | +195x |
- )+ ui_args = ui_args, |
||
| 144 | -78x - | +288 | +195x |
- colnames(mm)[colnames(mm) == "global_filters"] <- "Global filters"+ transformers = transformers |
| 145 | +289 |
-
+ ), |
||
| 146 | -78x - | +290 | +195x |
- mm+ class = "teal_module" |
| 147 | +291 |
- })+ ) |
||
| 148 | +292 |
- })+ } |
||
| 149 | +293 | |||
| 294 | ++ |
+ #' @rdname teal_modules+ |
+ ||
| 295 | ++ |
+ #' @export+ |
+ ||
| 296 | ++ |
+ #'+ |
+ ||
| 297 | ++ |
+ modules <- function(..., label = "root") {
+ |
+ ||
| 150 | -77x - | +298 | +135x |
- output$slices_table <- renderTable(+ checkmate::assert_string(label) |
| 151 | -77x - | +299 | +133x |
- expr = {
+ submodules <- list(...) |
| 152 | -86x - | +300 | +133x |
- logger::log_debug("filter_manager_srv@1 rendering slices_table.")
+ if (any(vapply(submodules, is.character, FUN.VALUE = logical(1)))) {
|
| 153 | -86x - | +301 | +2x |
- mm <- mapping_table()+ stop(+ |
+
| 302 | +2x | +
+ "The only character argument to modules() must be 'label' and it must be named, ",+ |
+ ||
| 303 | +2x | +
+ "change modules('lab', ...) to modules(label = 'lab', ...)"
|
||
| 154 | +304 |
-
+ ) |
||
| 155 | +305 |
- # Display logical values as UTF characters.+ } |
||
| 156 | -78x - | +|||
| 306 | +
- mm[] <- lapply(mm, ifelse, yes = intToUtf8(9989), no = intToUtf8(10060))+ |
|||
| 157 | -78x - | +307 | +131x |
- mm[] <- lapply(mm, function(x) ifelse(is.na(x), intToUtf8(128306), x))+ checkmate::assert_list(submodules, min.len = 1, any.missing = FALSE, types = c("teal_module", "teal_modules"))
|
| 158 | +308 |
-
+ # name them so we can more easily access the children |
||
| 159 | +309 |
- # Display placeholder if no filters defined.+ # beware however that the label of the submodules should not be changed as it must be kept synced |
||
| 160 | -78x - | +310 | +128x |
- if (nrow(mm) == 0L) {
+ labels <- vapply(submodules, function(submodule) submodule$label, character(1)) |
| 161 | -54x - | +311 | +128x |
- mm <- data.frame(`Filter manager` = "No filters specified.", check.names = FALSE)+ names(submodules) <- get_unique_labels(labels) |
| 162 | -54x - | +312 | +128x |
- rownames(mm) <- ""+ structure( |
| 163 | -+ | |||
| 313 | +128x |
- }+ list( |
||
| 164 | -78x - | +314 | +128x |
- mm+ label = label,+ |
+
| 315 | +128x | +
+ children = submodules |
||
| 165 | +316 |
- },+ ), |
||
| 166 | -77x - | +317 | +128x |
- rownames = TRUE+ class = "teal_modules" |
| 167 | +318 |
- )+ ) |
||
| 168 | +319 |
-
+ } |
||
| 169 | -77x - | +|||
| 320 | +
- mapping_table # for testing purpose+ |
|||
| 170 | +321 |
- })+ # printing methods ---- |
||
| 171 | +322 |
- }+ |
||
| 172 | +323 |
-
+ #' @rdname teal_modules |
||
| 173 | +324 |
- #' @rdname module_filter_manager+ #' @export |
||
| 174 | +325 |
- srv_module_filter_manager <- function(id, module_fd, slices_global) {
+ format.teal_module <- function(x, indent = 0, ...) {
|
||
| 175 | -102x - | +326 | +3x |
- checkmate::assert_string(id)+ paste0(paste(rep(" ", indent), collapse = ""), "+ ", x$label, "\n", collapse = "")
|
| 176 | -102x - | +|||
| 327 | +
- assert_reactive(module_fd)+ } |
|||
| 177 | -102x - | +|||
| 328 | +
- checkmate::assert_class(slices_global, ".slicesGlobal")+ |
|||
| 178 | +329 | |||
| 179 | -102x - | +|||
| 330 | +
- moduleServer(id, function(input, output, session) {
+ #' @rdname teal_modules |
|||
| 180 | -102x - | +|||
| 331 | +
- logger::log_debug("srv_module_filter_manager initializing for module: { id }.")
+ #' @export |
|||
| 181 | +332 |
- # Track filter global and local states.+ print.teal_module <- function(x, ...) {
|
||
| 182 | -102x - | +|||
| 333 | +! |
- slices_global_module <- reactive({
+ cat(format(x, ...)) |
||
| 183 | -183x - | +|||
| 334 | +! |
- slices_global$slices_get(module_label = id)+ invisible(x) |
||
| 184 | +335 |
- })+ } |
||
| 185 | -102x - | +|||
| 336 | +
- slices_module <- reactive(req(module_fd())$get_filter_state())+ |
|||
| 186 | +337 | |||
| 187 | -102x - | +|||
| 338 | +
- module_fd_previous <- reactiveVal(NULL)+ #' @rdname teal_modules |
|||
| 188 | +339 |
-
+ #' @export |
||
| 189 | +340 |
- # Set (reactively) available filters for the module.+ format.teal_modules <- function(x, indent = 0, ...) {
|
||
| 190 | -102x - | +341 | +1x |
- obs1 <- observeEvent(module_fd(), priority = 1, {
+ paste( |
| 191 | -83x - | +342 | +1x |
- logger::log_debug("srv_module_filter_manager@1 setting initial slices for module: { id }.")
+ c( |
| 192 | -+ | |||
| 343 | +1x |
- # Filters relevant for the module in module-specific app.+ paste0(rep(" ", indent), "+ ", x$label, "\n"),
|
||
| 193 | -83x - | +344 | +1x |
- slices <- slices_global_module()+ unlist(lapply(x$children, format, indent = indent + 1, ...)) |
| 194 | +345 |
-
+ ),+ |
+ ||
| 346 | +1x | +
+ collapse = "" |
||
| 195 | +347 |
- # Clean up previous filter states and refresh cache of previous module_fd with current+ ) |
||
| 196 | -3x - | +|||
| 348 | +
- if (!is.null(module_fd_previous())) module_fd_previous()$finalize()+ } |
|||
| 197 | -83x - | +|||
| 349 | +
- module_fd_previous(module_fd())+ |
|||
| 198 | +350 |
-
+ #' @param modules (`teal_module` or `teal_modules`) |
||
| 199 | +351 |
- # Setting filter states from slices_global:+ #' @rdname teal_modules |
||
| 200 | +352 |
- # 1. when app initializes slices_global set to initial filters (specified by app developer)+ #' @examples |
||
| 201 | +353 |
- # 2. when data reinitializes slices_global reflects latest filter states+ #' # change the module's datanames |
||
| 202 | +354 |
-
+ #' set_datanames(module(datanames = "all"), "a") |
||
| 203 | -83x - | +|||
| 355 | +
- module_fd()$set_filter_state(slices)+ #' |
|||
| 204 | +356 |
-
+ #' # change modules' datanames |
||
| 205 | +357 |
- # irrelevant filters are discarded in FilteredData$set_available_teal_slices+ #' set_datanames( |
||
| 206 | +358 |
- # it means we don't need to subset slices_global$all_slices() from filters refering to irrelevant datasets+ #' modules( |
||
| 207 | -83x - | +|||
| 359 | +
- module_fd()$set_available_teal_slices(slices_global$all_slices)+ #' module(datanames = "all"), |
|||
| 208 | +360 |
-
+ #' module(datanames = "a") |
||
| 209 | +361 |
- # this needed in filter_manager_srv+ #' ), |
||
| 210 | -83x - | +|||
| 362 | +
- slices_global$module_slices_api_set(+ #' "b" |
|||
| 211 | -83x - | +|||
| 363 | +
- id,+ #' ) |
|||
| 212 | -83x - | +|||
| 364 | +
- list(+ #' @export |
|||
| 213 | -83x - | +|||
| 365 | +
- get_available_teal_slices = module_fd()$get_available_teal_slices(),+ set_datanames <- function(modules, datanames) {
|
|||
| 214 | -83x - | +|||
| 366 | +! |
- set_filter_state = module_fd()$set_filter_state, # for testing purpose+ checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"))
|
||
| 215 | -83x - | +|||
| 367 | +! |
- get_filter_state = module_fd()$get_filter_state # for testing purpose+ if (inherits(modules, "teal_modules")) {
|
||
| 216 | -+ | |||
| 368 | +! |
- )+ modules$children <- lapply(modules$children, set_datanames, datanames) |
||
| 217 | +369 |
- )+ } else {
|
||
| 218 | -+ | |||
| 370 | +! |
- })+ if (identical(modules$datanames, "all")) {
|
||
| 219 | -+ | |||
| 371 | +! |
-
+ modules$datanames <- datanames |
||
| 220 | +372 |
- # Update global state and mapping matrix when module filters change.+ } else {
|
||
| 221 | -102x - | +|||
| 373 | +! |
- obs2 <- observeEvent(slices_module(), priority = 0, {
+ warning( |
||
| 222 | -105x - | +|||
| 374 | +! |
- this_slices <- slices_module()+ "Not possible to modify datanames of the module ", modules$label, |
||
| 223 | -105x - | +|||
| 375 | +! |
- slices_global$slices_append(this_slices) # append new slices to the all_slices list+ ". set_datanames() can only change datanames if it was set to \"all\".", |
||
| 224 | -105x - | +|||
| 376 | +! |
- mapping_elem <- setNames(nm = id, list(vapply(this_slices, `[[`, character(1L), "id")))+ call. = FALSE |
||
| 225 | -105x - | +|||
| 377 | +
- slices_global$slices_active(mapping_elem)+ ) |
|||
| 226 | +378 |
- })+ } |
||
| 227 | +379 |
-
+ } |
||
| 228 | -102x - | +|||
| 380 | +! |
- obs3 <- observeEvent(slices_global_module(), {
+ modules |
||
| 229 | -125x - | +|||
| 381 | +
- global_vs_module <- setdiff_teal_slices(slices_global_module(), slices_module())+ } |
|||
| 230 | -125x - | +|||
| 382 | +
- module_vs_global <- setdiff_teal_slices(slices_module(), slices_global_module())+ |
|||
| 231 | -116x - | +|||
| 383 | +
- if (length(global_vs_module) || length(module_vs_global)) {
+ #' @rdname teal_modules |
|||
| 232 | +384 |
- # Comment: (Nota Bene) Normally new filters for a module are added through module-filter-panel, and slices+ #' @export |
||
| 233 | +385 |
- # global are updated automatically so slices_module -> slices_global_module are equal.+ print.teal_modules <- print.teal_module |
||
| 234 | +386 |
- # this if is valid only when a change is made on the global level so the change needs to be propagated down+ |
||
| 235 | +387 |
- # to the module (for example through snapshot manager). If it happens both slices are different- |
- ||
| 236 | -13x - | -
- logger::log_debug("srv_module_filter_manager@3 (N.B.) global state has changed for a module:{ id }.")
- |
- ||
| 237 | -13x - | -
- module_fd()$clear_filter_states()- |
- ||
| 238 | -13x - | -
- module_fd()$set_filter_state(slices_global_module())+ |
||
| 239 | +388 |
- }+ # utilities ---- |
||
| 240 | +389 |
- })+ ## subset or modify modules ---- |
||
| 241 | +390 | |||
| 242 | -102x - | -
- slices_module # returned for testing purpose- |
- ||
| 243 | +391 |
- })+ #' Append a `teal_module` to `children` of a `teal_modules` object |
||
| 244 | +392 |
- }+ #' @keywords internal |
||
| 245 | +393 |
-
+ #' @param modules (`teal_modules`) |
||
| 246 | +394 |
- #' @importFrom shiny reactiveVal reactiveValues+ #' @param module (`teal_module`) object to be appended onto the children of `modules` |
||
| 247 | +395 |
- methods::setOldClass("reactiveVal")
+ #' @return A `teal_modules` object with `module` appended. |
||
| 248 | +396 |
- methods::setOldClass("reactivevalues")
+ append_module <- function(modules, module) {
|
||
| 249 | -+ | |||
| 397 | +8x |
-
+ checkmate::assert_class(modules, "teal_modules") |
||
| 250 | -+ | |||
| 398 | +6x |
- #' @importFrom methods new+ checkmate::assert_class(module, "teal_module") |
||
| 251 | -+ | |||
| 399 | +4x |
- #' @rdname module_filter_manager+ modules$children <- c(modules$children, list(module)) |
||
| 252 | -+ | |||
| 400 | +4x |
- .slicesGlobal <- methods::setRefClass(".slicesGlobal", # nolint: object_name.
+ labels <- vapply(modules$children, function(submodule) submodule$label, character(1)) |
||
| 253 | -+ | |||
| 401 | +4x |
- fields = list(+ names(modules$children) <- get_unique_labels(labels) |
||
| 254 | -+ | |||
| 402 | +4x |
- all_slices = "reactiveVal",+ modules |
||
| 255 | +403 |
- module_slices_api = "reactivevalues"+ } |
||
| 256 | +404 |
- ),+ |
||
| 257 | +405 |
- methods = list(+ #' Extract/Remove module(s) of specific class |
||
| 258 | +406 |
- initialize = function(slices = teal_slices(), module_labels) {
- |
- ||
| 259 | -77x - | -
- shiny::isolate({
- |
- ||
| 260 | -77x - | -
- checkmate::assert_class(slices, "teal_slices")+ #' |
||
| 261 | +407 |
- # needed on init to not mix "global_filters" with module-specific-slots- |
- ||
| 262 | -77x - | -
- if (isTRUE(attr(slices, "module_specific"))) {
- |
- ||
| 263 | -11x - | -
- old_mapping <- attr(slices, "mapping")- |
- ||
| 264 | -11x - | -
- new_mapping <- sapply(module_labels, simplify = FALSE, function(module_label) {
- |
- ||
| 265 | -20x - | -
- unique(unlist(old_mapping[c(module_label, "global_filters")]))+ #' Given a `teal_module` or a `teal_modules`, return the elements of the structure according to `class`. |
||
| 266 | +408 |
- })- |
- ||
| 267 | -11x - | -
- attr(slices, "mapping") <- new_mapping+ #' |
||
| 268 | +409 |
- }- |
- ||
| 269 | -77x - | -
- .self$all_slices <<- shiny::reactiveVal(slices)- |
- ||
| 270 | -77x - | -
- .self$module_slices_api <<- shiny::reactiveValues()- |
- ||
| 271 | -77x - | -
- .self$slices_append(slices)- |
- ||
| 272 | -77x - | -
- .self$slices_active(attr(slices, "mapping"))+ #' @param modules (`teal_modules`) |
||
| 273 | -77x - | +|||
| 410 | +
- invisible(.self)+ #' @param class The class name of `teal_module` to be extracted or dropped. |
|||
| 274 | +411 |
- })+ #' @keywords internal |
||
| 275 | +412 |
- },+ #' @return |
||
| 276 | +413 |
- is_module_specific = function() {
+ #' - For `extract_module`, a `teal_module` of class `class` or `teal_modules` containing modules of class `class`. |
||
| 277 | -268x - | +|||
| 414 | +
- isTRUE(attr(.self$all_slices(), "module_specific"))+ #' - For `drop_module`, the opposite, which is all `teal_modules` of class other than `class`. |
|||
| 278 | +415 |
- },+ #' @rdname module_management |
||
| 279 | +416 |
- module_slices_api_set = function(module_label, functions_list) {
+ extract_module <- function(modules, class) {
|
||
| 280 | -83x - | +417 | +24x |
- shiny::isolate({
+ if (inherits(modules, class)) {
|
| 281 | -83x - | +|||
| 418 | +! |
- if (!.self$is_module_specific()) {
+ modules |
||
| 282 | -67x - | +419 | +24x |
- module_label <- "global_filters"+ } else if (inherits(modules, "teal_module")) {
|
| 283 | -+ | |||
| 420 | +13x |
- }+ NULL |
||
| 284 | -83x - | +421 | +11x |
- if (!identical(.self$module_slices_api[[module_label]], functions_list)) {
+ } else if (inherits(modules, "teal_modules")) {
|
| 285 | -83x - | +422 | +11x |
- .self$module_slices_api[[module_label]] <- functions_list+ Filter(function(x) length(x) > 0L, lapply(modules$children, extract_module, class)) |
| 286 | +423 |
- }+ } |
||
| 287 | -83x - | +|||
| 424 | +
- invisible(.self)+ } |
|||
| 288 | +425 |
- })+ |
||
| 289 | +426 |
- },+ #' @keywords internal |
||
| 290 | +427 |
- slices_deactivate_all = function(module_label) {
+ #' @return `teal_modules` |
||
| 291 | -! | +|||
| 428 | +
- shiny::isolate({
+ #' @rdname module_management |
|||
| 292 | -! | +|||
| 429 | +
- new_slices <- .self$all_slices()+ drop_module <- function(modules, class) {
|
|||
| 293 | +430 | ! |
- old_mapping <- attr(new_slices, "mapping")- |
- |
| 294 | -- |
-
+ if (inherits(modules, class)) {
|
||
| 295 | +431 | ! |
- new_mapping <- if (.self$is_module_specific()) {
+ NULL |
|
| 296 | +432 | ! |
- new_module_mapping <- setNames(nm = module_label, list(character(0)))+ } else if (inherits(modules, "teal_module")) {
|
|
| 297 | +433 | ! |
- modifyList(old_mapping, new_module_mapping)+ modules |
|
| 298 | +434 | ! |
- } else if (missing(module_label)) {
+ } else if (inherits(modules, "teal_modules")) {
|
|
| 299 | +435 | ! |
- lapply(+ do.call( |
|
| 300 | +436 | ! |
- attr(.self$all_slices(), "mapping"),+ "modules", |
|
| 301 | +437 | ! |
- function(x) character(0)+ c(Filter(function(x) length(x) > 0L, lapply(modules$children, drop_module, class)), label = modules$label) |
|
| 302 | +438 |
- )+ ) |
||
| 303 | +439 |
- } else {
- |
- ||
| 304 | -! | -
- old_mapping[[module_label]] <- character(0)- |
- ||
| 305 | -! | -
- old_mapping+ } |
||
| 306 | +440 |
- }+ } |
||
| 307 | +441 | |||
| 308 | -! | -
- if (!identical(new_mapping, old_mapping)) {
- |
- ||
| 309 | -! | -
- logger::log_debug(".slicesGlobal@slices_deactivate_all: deactivating all slices.")
- |
- ||
| 310 | -! | -
- attr(new_slices, "mapping") <- new_mapping- |
- ||
| 311 | -! | -
- .self$all_slices(new_slices)- |
- ||
| 312 | +442 |
- }- |
- ||
| 313 | -! | -
- invisible(.self)+ ## read modules ---- |
||
| 314 | +443 |
- })+ |
||
| 315 | +444 |
- },+ #' Does the object make use of the `arg` |
||
| 316 | +445 |
- slices_active = function(mapping_elem) {
- |
- ||
| 317 | -185x - | -
- shiny::isolate({
+ #' |
||
| 318 | -185x - | +|||
| 446 | +
- if (.self$is_module_specific()) {
+ #' @param modules (`teal_module` or `teal_modules`) object |
|||
| 319 | -36x - | +|||
| 447 | +
- new_mapping <- modifyList(attr(.self$all_slices(), "mapping"), mapping_elem)+ #' @param arg (`character(1)`) names of the arguments to be checked against formals of `teal` modules. |
|||
| 320 | +448 |
- } else {
+ #' @return `logical` whether the object makes use of `arg`. |
||
| 321 | -149x - | +|||
| 449 | +
- new_mapping <- setNames(nm = "global_filters", list(unique(unlist(mapping_elem))))+ #' @rdname is_arg_used |
|||
| 322 | +450 |
- }+ #' @keywords internal |
||
| 323 | +451 |
-
+ is_arg_used <- function(modules, arg) {
|
||
| 324 | -185x - | +452 | +476x |
- if (!identical(new_mapping, attr(.self$all_slices(), "mapping"))) {
+ checkmate::assert_string(arg) |
| 325 | -128x - | +453 | +473x |
- mapping_modules <- toString(names(new_mapping))+ if (inherits(modules, "teal_modules")) {
|
| 326 | -128x - | +454 | +18x |
- logger::log_debug(".slicesGlobal@slices_active: changing mapping for module(s): { mapping_modules }.")
+ any(unlist(lapply(modules$children, is_arg_used, arg))) |
| 327 | -128x - | +455 | +455x |
- new_slices <- .self$all_slices()+ } else if (inherits(modules, "teal_module")) {
|
| 328 | -128x - | +456 | +30x |
- attr(new_slices, "mapping") <- new_mapping+ is_arg_used(modules$server, arg) || is_arg_used(modules$ui, arg) |
| 329 | -128x - | +457 | +425x |
- .self$all_slices(new_slices)+ } else if (is.function(modules)) {
|
| 330 | -+ | |||
| 458 | +423x |
- }+ isTRUE(arg %in% names(formals(modules))) |
||
| 331 | +459 |
-
+ } else {
|
||
| 332 | -185x - | +460 | +2x |
- invisible(.self)+ stop("is_arg_used function not implemented for this object")
|
| 333 | +461 |
- })+ } |
||
| 334 | +462 |
- },+ } |
||
| 335 | +463 |
- # - only new filters are appended to the $all_slices+ |
||
| 336 | +464 |
- # - mapping is not updated here+ |
||
| 337 | +465 |
- slices_append = function(slices, activate = FALSE) {
+ #' Get module depth |
||
| 338 | -185x - | +|||
| 466 | +
- shiny::isolate({
+ #' |
|||
| 339 | -185x - | +|||
| 467 | +
- if (!is.teal_slices(slices)) {
+ #' Depth starts at 0, so a single `teal.module` has depth 0. |
|||
| 340 | -! | +|||
| 468 | +
- slices <- as.teal_slices(slices)+ #' Nesting it increases overall depth by 1. |
|||
| 341 | +469 |
- }+ #' |
||
| 342 | +470 |
-
+ #' @inheritParams init |
||
| 343 | +471 |
- # to make sure that we don't unnecessary trigger $all_slices <reactiveVal>+ #' @param depth optional integer determining current depth level |
||
| 344 | -185x - | +|||
| 472 | +
- new_slices <- setdiff_teal_slices(slices, .self$all_slices())+ #' |
|||
| 345 | -185x - | +|||
| 473 | +
- old_mapping <- attr(.self$all_slices(), "mapping")+ #' @return Depth level for given module. |
|||
| 346 | -185x - | +|||
| 474 | +
- if (length(new_slices)) {
+ #' @keywords internal |
|||
| 347 | -6x - | +|||
| 475 | +
- new_ids <- vapply(new_slices, `[[`, character(1L), "id")+ modules_depth <- function(modules, depth = 0L) {
|
|||
| 348 | -6x - | +476 | +12x |
- logger::log_debug(".slicesGlobal@slices_append: appending new slice(s): { new_ids }.")
+ checkmate::assert_multi_class(modules, c("teal_module", "teal_modules"))
|
| 349 | -6x - | +477 | +12x |
- slices_ids <- vapply(.self$all_slices(), `[[`, character(1L), "id")+ checkmate::assert_int(depth, lower = 0) |
| 350 | -6x - | +478 | +11x |
- lapply(new_slices, function(slice) {
+ if (inherits(modules, "teal_modules")) {
|
| 351 | -+ | |||
| 479 | +4x |
- # In case the new state has the same id as an existing one, add a suffix+ max(vapply(modules$children, modules_depth, integer(1), depth = depth + 1L)) |
||
| 352 | -6x - | +|||
| 480 | +
- if (slice$id %in% slices_ids) {
+ } else {
|
|||
| 353 | -1x - | +481 | +7x |
- slice$id <- utils::tail(make.unique(c(slices_ids, slice$id), sep = "_"), 1)+ depth |
| 354 | +482 |
- }+ } |
||
| 355 | +483 |
- })+ } |
||
| 356 | +484 | |||
| 357 | -6x - | -
- new_slices_all <- c(.self$all_slices(), new_slices)- |
- ||
| 358 | -6x - | -
- attr(new_slices_all, "mapping") <- old_mapping- |
- ||
| 359 | -6x - | +|||
| 485 | +
- .self$all_slices(new_slices_all)+ #' Retrieve labels from `teal_modules` |
|||
| 360 | +486 |
- }+ #' |
||
| 361 | +487 |
-
+ #' @param modules (`teal_modules`) |
||
| 362 | -185x - | +|||
| 488 | +
- invisible(.self)+ #' @return A `list` containing the labels of the modules. If the modules are nested, |
|||
| 363 | +489 |
- })+ #' the function returns a nested `list` of labels. |
||
| 364 | +490 |
- },+ #' @keywords internal |
||
| 365 | +491 |
- slices_get = function(module_label) {
+ module_labels <- function(modules) {
|
||
| 366 | -274x - | +492 | +185x |
- if (missing(module_label)) {
+ if (inherits(modules, "teal_modules")) {
|
| 367 | -! | +|||
| 493 | +80x |
- .self$all_slices()+ lapply(modules$children, module_labels) |
||
| 368 | +494 |
- } else {
- |
- ||
| 369 | -274x - | -
- module_ids <- unlist(attr(.self$all_slices(), "mapping")[c(module_label, "global_filters")])+ } else {
|
||
| 370 | -274x - | +495 | +105x |
- Filter(+ modules$label |
| 371 | -274x - | +|||
| 496 | +
- function(slice) slice$id %in% module_ids,+ } |
|||
| 372 | -274x - | +|||
| 497 | +
- .self$all_slices()+ } |
|||
| 373 | +498 |
- )+ |
||
| 374 | +499 |
- }+ #' Retrieve `teal_bookmarkable` attribute from `teal_modules` |
||
| 375 | +500 |
- },+ #' |
||
| 376 | +501 |
- slices_set = function(slices) {
+ #' @param modules (`teal_modules` or `teal_module`) object |
||
| 377 | -7x - | +|||
| 502 | +
- shiny::isolate({
+ #' @return named list of the same structure as `modules` with `TRUE` or `FALSE` values indicating |
|||
| 378 | -7x - | +|||
| 503 | +
- if (!is.teal_slices(slices)) {
+ #' whether the module is bookmarkable. |
|||
| 379 | -! | +|||
| 504 | +
- slices <- as.teal_slices(slices)+ #' @keywords internal |
|||
| 380 | +505 |
- }+ modules_bookmarkable <- function(modules) {
|
||
| 381 | -7x - | +506 | +185x |
- .self$all_slices(slices)+ checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"))
|
| 382 | -7x - | -
- invisible(.self)- |
- ||
| 383 | -+ | 507 | +185x |
- })+ if (inherits(modules, "teal_modules")) {
|
| 384 | -+ | |||
| 508 | +80x |
- },+ setNames( |
||
| 385 | -+ | |||
| 509 | +80x |
- show = function() {
+ lapply(modules$children, modules_bookmarkable), |
||
| 386 | -! | +|||
| 510 | +80x |
- shiny::isolate(print(.self$all_slices()))+ vapply(modules$children, `[[`, "label", FUN.VALUE = character(1)) |
||
| 387 | -! | +|||
| 511 | +
- invisible(.self)+ ) |
|||
| 388 | +512 |
- }+ } else {
|
||
| 389 | -+ | |||
| 513 | +105x |
- )+ attr(modules, "teal_bookmarkable", exact = TRUE) |
||
| 390 | +514 |
- )+ } |
||
| 391 | +515 |
- # todo: prevent any teal_slices attribute except mapping+ } |
| 1 |
- #' Calls all `modules`+ #' Landing popup module |
||
| 3 |
- #' On the UI side each `teal_modules` is translated to a `tabsetPanel` and each `teal_module` is a+ #' @description Creates a landing welcome popup for `teal` applications. |
||
| 4 |
- #' `tabPanel`. Both, UI and server are called recursively so that each tab is a separate module and+ #' |
||
| 5 |
- #' reflect nested structure of `modules` argument.+ #' This module is used to display a popup dialog when the application starts. |
||
| 6 |
- #'+ #' The dialog blocks access to the application and must be closed with a button before the application can be viewed. |
||
| 7 |
- #' @name module_teal_module+ #' |
||
| 8 |
- #'+ #' @param label (`character(1)`) Label of the module. |
||
| 9 |
- #' @inheritParams module_teal+ #' @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. |
||
| 11 |
- #' @param data_rv (`reactive` returning `teal_data`)+ #' Passed to `...` of `shiny::modalDialog`. See examples. |
||
| 12 |
- #'+ #' @param buttons (`shiny.tag` or `shiny.tag.list`) Typically a `modalButton` or `actionButton`. See examples. |
||
| 13 |
- #' @param slices_global (`reactiveVal` returning `modules_teal_slices`)+ #' |
||
| 14 |
- #' see [`module_filter_manager`]+ #' @return A `teal_module` (extended with `teal_landing_module` class) to be used in `teal` applications. |
||
| 16 |
- #' @param depth (`integer(1)`)+ #' @examples |
||
| 17 |
- #' number which helps to determine depth of the modules nesting.+ #' app1 <- init( |
||
| 18 |
- #'+ #' data = teal_data(iris = iris), |
||
| 19 |
- #' @param datasets (`reactive` returning `FilteredData` or `NULL`)+ #' modules = modules( |
||
| 20 |
- #' When `datasets` is passed from the parent module (`srv_teal`) then `dataset` is a singleton+ #' example_module() |
||
| 21 |
- #' which implies in filter-panel to be "global". When `NULL` then filter-panel is "module-specific".+ #' ), |
||
| 22 |
- #'+ #' landing_popup = landing_popup_module( |
||
| 23 |
- #' @param data_load_status (`reactive` returning `character`)+ #' content = "A place for the welcome message or a disclaimer statement.", |
||
| 24 |
- #' Determines action dependent on a data loading status:+ #' buttons = modalButton("Proceed")
|
||
| 25 |
- #' - `"ok"` when `teal_data` is returned from the data loading.+ #' ) |
||
| 26 |
- #' - `"teal_data_module failed"` when [teal_data_module()] didn't return `teal_data`. Disables tabs buttons.+ #' ) |
||
| 27 |
- #' - `"external failed"` when a `reactive` passed to `srv_teal(data)` didn't return `teal_data`. Hides the whole tab+ #' if (interactive()) {
|
||
| 28 |
- #' panel.+ #' shinyApp(app1$ui, app1$server) |
||
| 29 |
- #'+ #' } |
||
| 30 |
- #' @return+ #' |
||
| 31 |
- #' output of currently active module.+ #' app2 <- init( |
||
| 32 |
- #' - `srv_teal_module.teal_module` returns `reactiveVal` containing output of the called module.+ #' data = teal_data(iris = iris), |
||
| 33 |
- #' - `srv_teal_module.teal_modules` returns output of module selected by `input$active_tab`.+ #' modules = modules( |
||
| 34 |
- #'+ #' example_module() |
||
| 35 |
- #' @keywords internal+ #' ), |
||
| 36 |
- NULL+ #' landing_popup = landing_popup_module( |
||
| 37 |
-
+ #' title = "Welcome", |
||
| 38 |
- #' @rdname module_teal_module+ #' content = tags$b( |
||
| 39 |
- ui_teal_module <- function(id, modules, depth = 0L) {
+ #' "A place for the welcome message or a disclaimer statement.", |
||
| 40 | -! | +
- checkmate::assert_multi_class(modules, c("teal_modules", "teal_module", "shiny.tag"))
+ #' style = "color: red;" |
|
| 41 | -! | +
- checkmate::assert_count(depth)+ #' ), |
|
| 42 | -! | +
- UseMethod("ui_teal_module", modules)
+ #' buttons = tagList( |
|
| 43 |
- }+ #' modalButton("Proceed"),
|
||
| 44 |
-
+ #' actionButton("read", "Read more",
|
||
| 45 |
- #' @rdname module_teal_module+ #' onclick = "window.open('http://google.com', '_blank')"
|
||
| 46 |
- #' @export+ #' ), |
||
| 47 |
- ui_teal_module.default <- function(id, modules, depth = 0L) {
+ #' actionButton("close", "Reject", onclick = "window.close()")
|
||
| 48 | -! | +
- stop("Modules class not supported: ", paste(class(modules), collapse = " "))
+ #' ) |
|
| 49 |
- }+ #' ) |
||
| 50 |
-
+ #' ) |
||
| 51 |
- #' @rdname module_teal_module+ #' |
||
| 52 |
- #' @export+ #' if (interactive()) {
|
||
| 53 |
- ui_teal_module.teal_modules <- function(id, modules, depth = 0L) {
+ #' shinyApp(app2$ui, app2$server) |
||
| 54 | -! | +
- ns <- NS(id)+ #' } |
|
| 55 | -! | +
- tags$div(+ #' |
|
| 56 | -! | +
- id = ns("wrapper"),
+ #' @export |
|
| 57 | -! | +
- do.call(+ landing_popup_module <- function(label = "Landing Popup", |
|
| 58 | -! | +
- tabsetPanel,+ title = NULL, |
|
| 59 | -! | +
- c(+ content = NULL, |
|
| 60 |
- # by giving an id, we can reactively respond to tab changes+ buttons = modalButton("Accept")) {
|
||
| 61 | ! |
- list(+ checkmate::assert_string(label) |
|
| 62 | ! |
- id = ns("active_tab"),
+ checkmate::assert_string(title, null.ok = TRUE) |
|
| 63 | ! |
- type = if (modules$label == "root") "pills" else "tabs"+ checkmate::assert_multi_class( |
|
| 64 | -+ | ! |
- ),+ content, |
| 65 | ! |
- lapply(+ classes = c("character", "shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE
|
|
| 66 | -! | +
- names(modules$children),+ ) |
|
| 67 | ! |
- function(module_id) {
+ checkmate::assert_multi_class(buttons, classes = c("shiny.tag", "shiny.tag.list"))
|
|
| 68 | -! | +
- module_label <- modules$children[[module_id]]$label+ |
|
| 69 | ! |
- if (is.null(module_label)) {
+ message("Initializing landing_popup_module")
|
|
| 70 | -! | +
- module_label <- icon("fas fa-database")
+
|
|
| 71 | -+ | ! |
- }+ module <- module( |
| 72 | ! |
- tabPanel(+ label = label, |
|
| 73 | ! |
- title = module_label,+ server = function(id) {
|
|
| 74 | ! |
- value = module_id, # when clicked this tab value changes input$<tabset panel id>+ moduleServer(id, function(input, output, session) {
|
|
| 75 | ! |
- ui_teal_module(+ showModal( |
|
| 76 | ! |
- id = ns(module_id),+ modalDialog( |
|
| 77 | ! |
- modules = modules$children[[module_id]],+ id = "landingpopup", |
|
| 78 | ! |
- depth = depth + 1L+ title = title, |
|
| 79 | -+ | ! |
- )+ content, |
| 80 | -+ | ! |
- )+ footer = buttons |
| 81 |
- }+ ) |
||
| 83 |
- )+ }) |
||
| 84 |
- )+ } |
||
| 86 | -+ | ! |
- }+ class(module) <- c("teal_module_landing", class(module))
|
| 87 | -+ | ! |
-
+ module |
| 88 |
- #' @rdname module_teal_module+ } |
| 89 | +1 |
- #' @export+ #' Validate that dataset has a minimum number of observations |
||
| 90 | +2 |
- ui_teal_module.teal_module <- function(id, modules, depth = 0L) {
- |
- ||
| 91 | -! | -
- ns <- NS(id)- |
- ||
| 92 | -! | -
- args <- c(list(id = ns("module")), modules$ui_args)
+ #' |
||
| 93 | +3 | - - | -||
| 94 | -! | -
- ui_teal <- tagList(- |
- ||
| 95 | -! | -
- div(- |
- ||
| 96 | -! | -
- id = ns("validate_datanames"),
- |
- ||
| 97 | -! | -
- ui_validate_reactive_teal_data(ns("validate_datanames"))
+ #' `r lifecycle::badge("stable")`
|
||
| 98 | +4 |
- ),- |
- ||
| 99 | -! | -
- shinyjs::hidden(- |
- ||
| 100 | -! | -
- tags$div(- |
- ||
| 101 | -! | -
- id = ns("transformer_failure_info"),
- |
- ||
| 102 | -! | -
- class = "teal_validated",- |
- ||
| 103 | -! | -
- div(- |
- ||
| 104 | -! | -
- class = "teal-output-warning",- |
- ||
| 105 | -! | -
- "One of transformers failed. Please fix and continue."+ #' |
||
| 106 | +5 |
- )+ #' This function is a wrapper for `shiny::validate`. |
||
| 107 | +6 |
- )+ #' |
||
| 108 | +7 |
- ),- |
- ||
| 109 | -! | -
- tags$div(- |
- ||
| 110 | -! | -
- id = ns("teal_module_ui"),
- |
- ||
| 111 | -! | -
- do.call(modules$ui, args)+ #' @param x (`data.frame`) |
||
| 112 | +8 |
- )+ #' @param min_nrow (`numeric(1)`) Minimum allowed number of rows in `x`. |
||
| 113 | +9 |
- )+ #' @param complete (`logical(1)`) Flag specifying whether to check only complete cases. Defaults to `FALSE`. |
||
| 114 | +10 | - - | -||
| 115 | -! | -
- div(- |
- ||
| 116 | -! | -
- id = id,- |
- ||
| 117 | -! | -
- class = "teal_module",- |
- ||
| 118 | -! | -
- uiOutput(ns("data_reactive"), inline = TRUE),
+ #' @param allow_inf (`logical(1)`) Flag specifying whether to allow infinite values. Defaults to `TRUE`. |
||
| 119 | -! | +|||
| 11 | +
- tagList(+ #' @param msg (`character(1)`) Additional message to display alongside the default message. |
|||
| 120 | -! | +|||
| 12 | +
- if (depth >= 2L) tags$div(style = "mt-6"),+ #' |
|||
| 121 | -! | +|||
| 13 | +
- if (!is.null(modules$datanames)) {
+ #' @export |
|||
| 122 | -! | +|||
| 14 | +
- fluidRow(+ #' |
|||
| 123 | -! | +|||
| 15 | +
- column(width = 9, ui_teal, class = "teal_primary_col"),+ #' @examples |
|||
| 124 | -! | +|||
| 16 | +
- column(+ #' library(teal) |
|||
| 125 | -! | +|||
| 17 | +
- width = 3,+ #' ui <- fluidPage( |
|||
| 126 | -! | +|||
| 18 | +
- ui_data_summary(ns("data_summary")),
+ #' sliderInput("len", "Max Length of Sepal",
|
|||
| 127 | -! | +|||
| 19 | +
- ui_filter_data(ns("filter_panel")),
+ #' min = 4.3, max = 7.9, value = 5 |
|||
| 128 | -! | +|||
| 20 | +
- ui_transform_data(ns("data_transform"), transformers = modules$transformers, class = "well"),
+ #' ), |
|||
| 129 | -! | +|||
| 21 | +
- class = "teal_secondary_col"+ #' plotOutput("plot")
|
|||
| 130 | +22 |
- )+ #' ) |
||
| 131 | +23 |
- )+ #' |
||
| 132 | +24 |
- } else {
+ #' server <- function(input, output) {
|
||
| 133 | -! | +|||
| 25 | +
- div(+ #' output$plot <- renderPlot({
|
|||
| 134 | -! | +|||
| 26 | +
- div(+ #' iris_df <- iris[iris$Sepal.Length <= input$len, ] |
|||
| 135 | -! | +|||
| 27 | +
- class = "teal_validated",+ #' validate_has_data( |
|||
| 136 | -! | +|||
| 28 | +
- uiOutput(ns("data_input_error"))
+ #' iris_df, |
|||
| 137 | +29 |
- ),+ #' min_nrow = 10, |
||
| 138 | -! | +|||
| 30 | +
- ui_teal+ #' complete = FALSE, |
|||
| 139 | +31 |
- )+ #' msg = "Please adjust Max Length of Sepal" |
||
| 140 | +32 |
- }+ #' ) |
||
| 141 | +33 |
- )+ #' |
||
| 142 | +34 |
- )+ #' hist(iris_df$Sepal.Length, breaks = 5) |
||
| 143 | +35 |
- }+ #' }) |
||
| 144 | +36 |
-
+ #' } |
||
| 145 | +37 |
- #' @rdname module_teal_module+ #' if (interactive()) {
|
||
| 146 | +38 |
- srv_teal_module <- function(id,+ #' shinyApp(ui, server) |
||
| 147 | +39 |
- data_rv,+ #' } |
||
| 148 | +40 |
- modules,+ #' |
||
| 149 | +41 |
- datasets = NULL,+ validate_has_data <- function(x, |
||
| 150 | +42 |
- slices_global,+ min_nrow = NULL, |
||
| 151 | +43 |
- reporter = teal.reporter::Reporter$new(),+ complete = FALSE, |
||
| 152 | +44 |
- data_load_status = reactive("ok"),
+ allow_inf = TRUE, |
||
| 153 | +45 |
- is_active = reactive(TRUE)) {
+ msg = NULL) {
|
||
| 154 | -179x - | +46 | +17x |
- checkmate::assert_string(id)+ checkmate::assert_string(msg, null.ok = TRUE) |
| 155 | -179x - | +47 | +15x |
- assert_reactive(data_rv)+ checkmate::assert_data_frame(x) |
| 156 | -179x - | +48 | +15x |
- checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"))
+ if (!is.null(min_nrow)) {
|
| 157 | -179x - | +49 | +15x |
- assert_reactive(datasets, null.ok = TRUE)+ if (complete) {
|
| 158 | -179x - | +50 | +5x |
- checkmate::assert_class(slices_global, ".slicesGlobal")+ complete_index <- stats::complete.cases(x) |
| 159 | -179x - | +51 | +5x |
- checkmate::assert_class(reporter, "Reporter")+ validate(need( |
| 160 | -179x - | +52 | +5x |
- assert_reactive(data_load_status)+ sum(complete_index) > 0 && nrow(x[complete_index, , drop = FALSE]) >= min_nrow, |
| 161 | -179x - | +53 | +5x |
- UseMethod("srv_teal_module", modules)
+ paste(c(paste("Number of complete cases is less than:", min_nrow), msg), collapse = "\n")
|
| 162 | +54 |
- }+ )) |
||
| 163 | +55 |
-
+ } else {
|
||
| 164 | -+ | |||
| 56 | +10x |
- #' @rdname module_teal_module+ validate(need( |
||
| 165 | -+ | |||
| 57 | +10x |
- #' @export+ nrow(x) >= min_nrow, |
||
| 166 | -+ | |||
| 58 | +10x |
- srv_teal_module.default <- function(id,+ paste( |
||
| 167 | -+ | |||
| 59 | +10x |
- data_rv,+ c(paste("Minimum number of records not met: >=", min_nrow, "records required."), msg),
|
||
| 168 | -+ | |||
| 60 | +10x |
- modules,+ collapse = "\n" |
||
| 169 | +61 |
- datasets = NULL,+ ) |
||
| 170 | +62 |
- slices_global,+ )) |
||
| 171 | +63 |
- reporter = teal.reporter::Reporter$new(),+ } |
||
| 172 | +64 |
- data_load_status = reactive("ok"),
+
|
||
| 173 | -+ | |||
| 65 | +10x |
- is_active = reactive(TRUE)) {
+ if (!allow_inf) {
|
||
| 174 | -! | +|||
| 66 | +6x |
- stop("Modules class not supported: ", paste(class(modules), collapse = " "))
+ validate(need( |
||
| 175 | -+ | |||
| 67 | +6x |
- }+ all(vapply(x, function(col) !is.numeric(col) || !any(is.infinite(col)), logical(1))),+ |
+ ||
| 68 | +6x | +
+ "Dataframe contains Inf values which is not allowed." |
||
| 176 | +69 |
-
+ )) |
||
| 177 | +70 |
- #' @rdname module_teal_module+ } |
||
| 178 | +71 |
- #' @export+ } |
||
| 179 | +72 |
- srv_teal_module.teal_modules <- function(id,+ } |
||
| 180 | +73 |
- data_rv,+ |
||
| 181 | +74 |
- modules,+ #' Validate that dataset has unique rows for key variables |
||
| 182 | +75 |
- datasets = NULL,+ #' |
||
| 183 | +76 |
- slices_global,+ #' `r lifecycle::badge("stable")`
|
||
| 184 | +77 |
- reporter = teal.reporter::Reporter$new(),+ #' |
||
| 185 | +78 |
- data_load_status = reactive("ok"),
+ #' This function is a wrapper for `shiny::validate`. |
||
| 186 | +79 |
- is_active = reactive(TRUE)) {
+ #' |
||
| 187 | -77x - | +|||
| 80 | +
- moduleServer(id = id, module = function(input, output, session) {
+ #' @param x (`data.frame`) |
|||
| 188 | -77x - | +|||
| 81 | +
- logger::log_debug("srv_teal_module.teal_modules initializing the module { deparse1(modules$label) }.")
+ #' @param key (`character`) Vector of ID variables from `x` that identify unique records. |
|||
| 189 | +82 |
-
+ #' |
||
| 190 | -77x - | +|||
| 83 | +
- observeEvent(data_load_status(), {
+ #' @export |
|||
| 191 | -70x - | +|||
| 84 | +
- tabs_selector <- sprintf("#%s li a", session$ns("active_tab"))
+ #' |
|||
| 192 | -70x - | +|||
| 85 | +
- if (identical(data_load_status(), "ok")) {
+ #' @examples |
|||
| 193 | -65x - | +|||
| 86 | +
- logger::log_debug("srv_teal_module@1 enabling modules tabs.")
+ #' iris$id <- rep(1:50, times = 3) |
|||
| 194 | -65x - | +|||
| 87 | +
- shinyjs::show("wrapper")
+ #' ui <- fluidPage( |
|||
| 195 | -65x - | +|||
| 88 | +
- shinyjs::enable(selector = tabs_selector)+ #' selectInput( |
|||
| 196 | -5x - | +|||
| 89 | +
- } else if (identical(data_load_status(), "teal_data_module failed")) {
+ #' inputId = "species", |
|||
| 197 | -5x - | +|||
| 90 | +
- logger::log_debug("srv_teal_module@1 disabling modules tabs.")
+ #' label = "Select species", |
|||
| 198 | -5x - | +|||
| 91 | +
- shinyjs::disable(selector = tabs_selector)+ #' choices = c("setosa", "versicolor", "virginica"),
|
|||
| 199 | -! | +|||
| 92 | +
- } else if (identical(data_load_status(), "external failed")) {
+ #' selected = "setosa", |
|||
| 200 | -! | +|||
| 93 | +
- logger::log_debug("srv_teal_module@1 hiding modules tabs.")
+ #' multiple = TRUE |
|||
| 201 | -! | +|||
| 94 | +
- shinyjs::hide("wrapper")
+ #' ), |
|||
| 202 | +95 |
- }+ #' plotOutput("plot")
|
||
| 203 | +96 |
- })+ #' ) |
||
| 204 | +97 |
-
+ #' server <- function(input, output) {
|
||
| 205 | -77x - | +|||
| 98 | +
- modules_output <- sapply(+ #' output$plot <- renderPlot({
|
|||
| 206 | -77x - | +|||
| 99 | +
- names(modules$children),+ #' iris_f <- iris[iris$Species %in% input$species, ] |
|||
| 207 | -77x - | +|||
| 100 | +
- function(module_id) {
+ #' validate_one_row_per_id(iris_f, key = c("id"))
|
|||
| 208 | -102x - | +|||
| 101 | +
- srv_teal_module(+ #' |
|||
| 209 | -102x - | +|||
| 102 | +
- id = module_id,+ #' hist(iris_f$Sepal.Length, breaks = 5) |
|||
| 210 | -102x - | +|||
| 103 | +
- data_rv = data_rv,+ #' }) |
|||
| 211 | -102x - | +|||
| 104 | +
- modules = modules$children[[module_id]],+ #' } |
|||
| 212 | -102x - | +|||
| 105 | +
- datasets = datasets,+ #' if (interactive()) {
|
|||
| 213 | -102x - | +|||
| 106 | +
- slices_global = slices_global,+ #' shinyApp(ui, server) |
|||
| 214 | -102x - | +|||
| 107 | +
- reporter = reporter,+ #' } |
|||
| 215 | -102x - | +|||
| 108 | +
- is_active = reactive(+ #' |
|||
| 216 | -102x - | +|||
| 109 | +
- is_active() &&+ validate_one_row_per_id <- function(x, key = c("USUBJID", "STUDYID")) {
|
|||
| 217 | -102x - | +|||
| 110 | +! |
- input$active_tab == module_id &&+ validate(need(!any(duplicated(x[key])), paste("Found more than one row per id.")))
|
||
| 218 | -102x - | +|||
| 111 | +
- identical(data_load_status(), "ok")+ } |
|||
| 219 | +112 |
- )+ |
||
| 220 | +113 |
- )+ #' Validates that vector includes all expected values |
||
| 221 | +114 |
- },+ #' |
||
| 222 | -77x - | +|||
| 115 | +
- simplify = FALSE+ #' `r lifecycle::badge("stable")`
|
|||
| 223 | +116 |
- )+ #' |
||
| 224 | +117 |
-
+ #' This function is a wrapper for `shiny::validate`. |
||
| 225 | -77x - | +|||
| 118 | +
- modules_output+ #' |
|||
| 226 | +119 |
- })+ #' @param x Vector of values to test. |
||
| 227 | +120 |
- }+ #' @param choices Vector to test against. |
||
| 228 | +121 |
-
+ #' @param msg (`character(1)`) Error message to display if some elements of `x` are not elements of `choices`. |
||
| 229 | +122 |
- #' @rdname module_teal_module+ #' |
||
| 230 | +123 |
#' @export |
||
| 231 | +124 |
- srv_teal_module.teal_module <- function(id,+ #' |
||
| 232 | +125 |
- data_rv,+ #' @examples |
||
| 233 | +126 |
- modules,+ #' ui <- fluidPage( |
||
| 234 | +127 |
- datasets = NULL,+ #' selectInput( |
||
| 235 | +128 |
- slices_global,+ #' "species", |
||
| 236 | +129 |
- reporter = teal.reporter::Reporter$new(),+ #' "Select species", |
||
| 237 | +130 |
- data_load_status = reactive("ok"),
+ #' choices = c("setosa", "versicolor", "virginica", "unknown species"),
|
||
| 238 | +131 |
- is_active = reactive(TRUE)) {
+ #' selected = "setosa", |
||
| 239 | -102x - | +|||
| 132 | +
- logger::log_debug("srv_teal_module.teal_module initializing the module: { deparse1(modules$label) }.")
+ #' multiple = FALSE |
|||
| 240 | -102x - | +|||
| 133 | +
- moduleServer(id = id, module = function(input, output, session) {
+ #' ), |
|||
| 241 | -102x - | +|||
| 134 | +
- module_out <- reactiveVal()+ #' verbatimTextOutput("summary")
|
|||
| 242 | +135 |
-
+ #' ) |
||
| 243 | -102x - | +|||
| 136 | +
- active_datanames <- reactive({
+ #' |
|||
| 244 | -79x - | +|||
| 137 | +
- .resolve_module_datanames(data = data_rv(), modules = modules)+ #' server <- function(input, output) {
|
|||
| 245 | +138 |
- })+ #' output$summary <- renderPrint({
|
||
| 246 | -102x - | +|||
| 139 | +
- if (is.null(datasets)) {
+ #' validate_in(input$species, iris$Species, "Species does not exist.") |
|||
| 247 | -20x - | +|||
| 140 | +
- datasets <- eventReactive(data_rv(), {
+ #' nrow(iris[iris$Species == input$species, ]) |
|||
| 248 | -16x - | +|||
| 141 | +
- req(inherits(data_rv(), "teal_data"))+ #' }) |
|||
| 249 | -16x - | +|||
| 142 | +
- logger::log_debug("srv_teal_module@1 initializing module-specific FilteredData")
+ #' } |
|||
| 250 | -16x - | +|||
| 143 | +
- teal_data_to_filtered_data(data_rv(), datanames = active_datanames())+ #' if (interactive()) {
|
|||
| 251 | +144 |
- })+ #' shinyApp(ui, server) |
||
| 252 | +145 |
- }+ #' } |
||
| 253 | +146 |
-
+ #' |
||
| 254 | +147 |
- # manage module filters on the module level+ validate_in <- function(x, choices, msg) {
+ |
+ ||
| 148 | +! | +
+ validate(need(length(x) > 0 && length(choices) > 0 && all(x %in% choices), msg)) |
||
| 255 | +149 |
- # important:+ } |
||
| 256 | +150 |
- # filter_manager_module_srv needs to be called before filter_panel_srv+ |
||
| 257 | +151 |
- # Because available_teal_slices is used in FilteredData$srv_available_slices (via srv_filter_panel)+ #' Validates that vector has length greater than 0 |
||
| 258 | +152 |
- # and if it is not set, then it won't be available in the srv_filter_panel+ #' |
||
| 259 | -102x - | +|||
| 153 | +
- srv_module_filter_manager(modules$label, module_fd = datasets, slices_global = slices_global)+ #' `r lifecycle::badge("stable")`
|
|||
| 260 | +154 |
-
+ #' |
||
| 261 | -102x - | +|||
| 155 | +
- call_once_when(is_active(), {
+ #' This function is a wrapper for `shiny::validate`. |
|||
| 262 | -76x - | +|||
| 156 | +
- filtered_teal_data <- srv_filter_data(+ #' |
|||
| 263 | -76x - | -
- "filter_panel",- |
- ||
| 264 | -76x - | +|||
| 157 | +
- datasets = datasets,+ #' @param x vector |
|||
| 265 | -76x - | +|||
| 158 | +
- active_datanames = active_datanames,+ #' @param msg message to display |
|||
| 266 | -76x - | +|||
| 159 | +
- data_rv = data_rv,+ #' |
|||
| 267 | -76x - | +|||
| 160 | +
- is_active = is_active+ #' @export |
|||
| 268 | +161 |
- )+ #' |
||
| 269 | -76x - | +|||
| 162 | +
- is_transformer_failed <- reactiveValues()+ #' @examples |
|||
| 270 | -76x - | +|||
| 163 | +
- transformed_teal_data <- srv_transform_data(+ #' data <- data.frame( |
|||
| 271 | -76x - | +|||
| 164 | +
- "data_transform",+ #' id = c(1:10, 11:20, 1:10), |
|||
| 272 | -76x - | +|||
| 165 | +
- data = filtered_teal_data,+ #' strata = rep(c("A", "B"), each = 15)
|
|||
| 273 | -76x - | +|||
| 166 | +
- transformers = modules$transformers,+ #' ) |
|||
| 274 | -76x - | +|||
| 167 | +
- modules = modules,+ #' ui <- fluidPage( |
|||
| 275 | -76x - | +|||
| 168 | +
- is_transformer_failed = is_transformer_failed+ #' selectInput("ref1", "Select strata1 to compare",
|
|||
| 276 | +169 |
- )+ #' choices = c("A", "B", "C"), selected = "A"
|
||
| 277 | -76x - | +|||
| 170 | +
- any_transformer_failed <- reactive({
+ #' ), |
|||
| 278 | -76x - | +|||
| 171 | +
- any(unlist(reactiveValuesToList(is_transformer_failed)))+ #' selectInput("ref2", "Select strata2 to compare",
|
|||
| 279 | +172 |
- })+ #' choices = c("A", "B", "C"), selected = "B"
|
||
| 280 | +173 |
-
+ #' ), |
||
| 281 | -76x - | +|||
| 174 | +
- observeEvent(any_transformer_failed(), {
+ #' verbatimTextOutput("arm_summary")
|
|||
| 282 | -76x - | +|||
| 175 | +
- if (isTRUE(any_transformer_failed())) {
+ #' ) |
|||
| 283 | -6x - | +|||
| 176 | +
- shinyjs::hide("teal_module_ui")
+ #' |
|||
| 284 | -6x - | +|||
| 177 | +
- shinyjs::hide("validate_datanames")
+ #' server <- function(input, output) {
|
|||
| 285 | -6x - | +|||
| 178 | +
- shinyjs::show("transformer_failure_info")
+ #' output$arm_summary <- renderText({
|
|||
| 286 | +179 |
- } else {
+ #' sample_1 <- data$id[data$strata == input$ref1] |
||
| 287 | -70x - | +|||
| 180 | +
- shinyjs::show("teal_module_ui")
+ #' sample_2 <- data$id[data$strata == input$ref2] |
|||
| 288 | -70x - | +|||
| 181 | +
- shinyjs::show("validate_datanames")
+ #' |
|||
| 289 | -70x - | +|||
| 182 | +
- shinyjs::hide("transformer_failure_info")
+ #' validate_has_elements(sample_1, "No subjects in strata1.") |
|||
| 290 | +183 |
- }+ #' validate_has_elements(sample_2, "No subjects in strata2.") |
||
| 291 | +184 |
- })+ #' |
||
| 292 | +185 |
-
+ #' paste0( |
||
| 293 | -76x - | +|||
| 186 | +
- module_teal_data <- reactive({
+ #' "Number of samples in: strata1=", length(sample_1), |
|||
| 294 | -84x - | +|||
| 187 | +
- req(inherits(transformed_teal_data(), "teal_data"))+ #' " comparions strata2=", length(sample_2) |
|||
| 295 | -78x - | +|||
| 188 | +
- all_teal_data <- transformed_teal_data()+ #' ) |
|||
| 296 | -78x - | +|||
| 189 | +
- module_datanames <- .resolve_module_datanames(data = all_teal_data, modules = modules)+ #' }) |
|||
| 297 | -78x - | +|||
| 190 | +
- .subset_teal_data(all_teal_data, module_datanames)+ #' } |
|||
| 298 | +191 |
- })+ #' if (interactive()) {
|
||
| 299 | +192 |
-
+ #' shinyApp(ui, server) |
||
| 300 | -76x - | +|||
| 193 | +
- srv_validate_reactive_teal_data(+ #' } |
|||
| 301 | -76x - | +|||
| 194 | +
- "validate_datanames",+ validate_has_elements <- function(x, msg) {
|
|||
| 302 | -76x - | +|||
| 195 | +! |
- data = module_teal_data,+ validate(need(length(x) > 0, msg)) |
||
| 303 | -76x - | +|||
| 196 | +
- modules = modules+ } |
|||
| 304 | +197 |
- )+ |
||
| 305 | +198 |
-
+ #' Validates no intersection between two vectors |
||
| 306 | -76x - | +|||
| 199 | +
- summary_table <- srv_data_summary("data_summary", module_teal_data)
+ #' |
|||
| 307 | +200 |
-
+ #' `r lifecycle::badge("stable")`
|
||
| 308 | +201 |
- # Call modules.+ #' |
||
| 309 | -76x - | +|||
| 202 | +
- if (!inherits(modules, "teal_module_previewer")) {
+ #' This function is a wrapper for `shiny::validate`. |
|||
| 310 | -76x - | +|||
| 203 | +
- obs_module <- call_once_when(+ #' |
|||
| 311 | -76x - | +|||
| 204 | +
- !is.null(module_teal_data()),+ #' @param x vector |
|||
| 312 | -76x - | +|||
| 205 | +
- ignoreNULL = TRUE,+ #' @param y vector |
|||
| 313 | -76x - | +|||
| 206 | +
- handlerExpr = {
+ #' @param msg (`character(1)`) message to display if `x` and `y` intersect |
|||
| 314 | -70x - | +|||
| 207 | +
- module_out(.call_teal_module(modules, datasets, module_teal_data, reporter))+ #' |
|||
| 315 | +208 |
- }+ #' @export |
||
| 316 | +209 |
- )+ #' |
||
| 317 | +210 |
- } else {
+ #' @examples |
||
| 318 | +211 |
- # Report previewer must be initiated on app start for report cards to be included in bookmarks.+ #' data <- data.frame( |
||
| 319 | +212 |
- # When previewer is delayed, cards are bookmarked only if previewer has been initiated (visited).+ #' id = c(1:10, 11:20, 1:10), |
||
| 320 | -! | +|||
| 213 | +
- module_out(.call_teal_module(modules, datasets, module_teal_data, reporter))+ #' strata = rep(c("A", "B", "C"), each = 10)
|
|||
| 321 | +214 |
- }+ #' ) |
||
| 322 | +215 |
-
+ #' |
||
| 323 | +216 |
- # todo: (feature request) add a ReporterCard to the reporter as an output from the teal_module+ #' ui <- fluidPage( |
||
| 324 | +217 |
- # how to determine if module returns a ReporterCard so that reportPreviewer is needed?+ #' selectInput("ref1", "Select strata1 to compare",
|
||
| 325 | +218 |
- # Should we insertUI of the ReportPreviewer then?+ #' choices = c("A", "B", "C"),
|
||
| 326 | +219 |
- # What about attr(module, "reportable") - similar to attr(module, "bookmarkable")+ #' selected = "A" |
||
| 327 | -76x - | +|||
| 220 | +
- if ("report" %in% names(module_out)) {
+ #' ), |
|||
| 328 | +221 |
- # (reactively) add card to the reporter+ #' selectInput("ref2", "Select strata2 to compare",
|
||
| 329 | +222 |
- }+ #' choices = c("A", "B", "C"),
|
||
| 330 | +223 |
- })+ #' selected = "B" |
||
| 331 | +224 |
-
+ #' ), |
||
| 332 | -102x - | +|||
| 225 | +
- module_out+ #' verbatimTextOutput("summary")
|
|||
| 333 | +226 |
- })+ #' ) |
||
| 334 | +227 |
- }+ #' |
||
| 335 | +228 |
-
+ #' server <- function(input, output) {
|
||
| 336 | +229 |
- # This function calls a module server function.+ #' output$summary <- renderText({
|
||
| 337 | +230 |
- .call_teal_module <- function(modules, datasets, filtered_teal_data, reporter) {
+ #' sample_1 <- data$id[data$strata == input$ref1] |
||
| 338 | +231 |
- # collect arguments to run teal_module+ #' sample_2 <- data$id[data$strata == input$ref2] |
||
| 339 | -70x - | +|||
| 232 | +
- args <- c(list(id = "module"), modules$server_args)+ #' |
|||
| 340 | -70x - | +|||
| 233 | +
- if (is_arg_used(modules$server, "reporter")) {
+ #' validate_no_intersection( |
|||
| 341 | -1x - | +|||
| 234 | +
- args <- c(args, list(reporter = reporter))+ #' sample_1, sample_2, |
|||
| 342 | +235 |
- }+ #' "subjects within strata1 and strata2 cannot overlap" |
||
| 343 | +236 |
-
+ #' ) |
||
| 344 | -70x - | +|||
| 237 | +
- if (is_arg_used(modules$server, "datasets")) {
+ #' paste0( |
|||
| 345 | -1x - | +|||
| 238 | +
- args <- c(args, datasets = datasets())+ #' "Number of subject in: reference treatment=", length(sample_1), |
|||
| 346 | -1x - | +|||
| 239 | +
- warning("datasets argument is not reactive and therefore it won't be updated when data is refreshed.")
+ #' " comparions treatment=", length(sample_2) |
|||
| 347 | +240 |
- }+ #' ) |
||
| 348 | +241 |
-
+ #' }) |
||
| 349 | -70x - | +|||
| 242 | +
- if (is_arg_used(modules$server, "data")) {
+ #' } |
|||
| 350 | -66x - | +|||
| 243 | +
- args <- c(args, data = list(filtered_teal_data))+ #' if (interactive()) {
|
|||
| 351 | +244 |
- }+ #' shinyApp(ui, server) |
||
| 352 | +245 |
-
+ #' } |
||
| 353 | -70x - | +|||
| 246 | +
- if (is_arg_used(modules$server, "filter_panel_api")) {
- |
- |||
| 354 | -1x - | -
- args <- c(args, filter_panel_api = teal.slice::FilterPanelAPI$new(datasets()))- |
- ||
| 355 | -- |
- }+ #' |
||
| 356 | +247 |
-
+ validate_no_intersection <- function(x, y, msg) {
|
||
| 357 | -70x - | +|||
| 248 | +! |
- if (is_arg_used(modules$server, "id")) {
+ validate(need(length(intersect(x, y)) == 0, msg)) |
||
| 358 | -70x - | +|||
| 249 | +
- do.call(modules$server, args)+ } |
|||
| 359 | +250 |
- } else {
+
|
||
| 360 | -! | +|||
| 251 | +
- do.call(callModule, c(args, list(module = modules$server)))+ |
|||
| 361 | +252 |
- }+ #' Validates that dataset contains specific variable |
||
| 362 | +253 |
- }+ #' |
||
| 363 | +254 |
-
+ #' `r lifecycle::badge("stable")`
|
||
| 364 | +255 |
- .resolve_module_datanames <- function(data, modules) {
+ #' |
||
| 365 | -157x - | +|||
| 256 | +
- stopifnot("data_rv must be teal_data object." = inherits(data, "teal_data"))
+ #' This function is a wrapper for `shiny::validate`. |
|||
| 366 | -157x - | +|||
| 257 | +
- if (is.null(modules$datanames) || identical(modules$datanames, "all")) {
+ #' |
|||
| 367 | -131x - | +|||
| 258 | +
- .topologically_sort_datanames(ls(teal.code::get_env(data)), teal.data::join_keys(data))+ #' @param data (`data.frame`) |
|||
| 368 | +259 |
- } else {
+ #' @param varname (`character(1)`) name of variable to check for in `data` |
||
| 369 | -26x - | +|||
| 260 | +
- intersect(+ #' @param msg (`character(1)`) message to display if `data` does not include `varname` |
|||
| 370 | -26x - | +|||
| 261 | +
- .include_parent_datanames(modules$datanames, teal.data::join_keys(data)),+ #' |
|||
| 371 | -26x - | +|||
| 262 | +
- ls(teal.code::get_env(data))+ #' @export |
|||
| 372 | +263 |
- )+ #' |
||
| 373 | +264 |
- }+ #' @examples |
||
| 374 | +265 |
- }+ #' data <- data.frame( |
||
| 375 | +266 |
-
+ #' one = rep("a", length.out = 20),
|
||
| 376 | +267 |
- #' Calls expression when condition is met+ #' two = rep(c("a", "b"), length.out = 20)
|
||
| 377 | +268 |
- #'+ #' ) |
||
| 378 | +269 |
- #' Function postpones `handlerExpr` to the moment when `eventExpr` (condition) returns `TRUE`,+ #' ui <- fluidPage( |
||
| 379 | +270 |
- #' otherwise nothing happens.+ #' selectInput( |
||
| 380 | +271 |
- #' @param eventExpr A (quoted or unquoted) logical expression that represents the event;+ #' "var", |
||
| 381 | +272 |
- #' this can be a simple reactive value like input$click, a call to a reactive expression+ #' "Select variable", |
||
| 382 | +273 |
- #' like dataset(), or even a complex expression inside curly braces.+ #' choices = c("one", "two", "three", "four"),
|
||
| 383 | +274 |
- #' @param ... additional arguments passed to `observeEvent` with the exception of `eventExpr` that is not allowed.+ #' selected = "one" |
||
| 384 | +275 |
- #' @inheritParams shiny::observeEvent+ #' ), |
||
| 385 | +276 |
- #'+ #' verbatimTextOutput("summary")
|
||
| 386 | +277 |
- #' @return An observer.+ #' ) |
||
| 387 | +278 |
#' |
||
| 388 | +279 |
- #' @keywords internal+ #' server <- function(input, output) {
|
||
| 389 | +280 |
- call_once_when <- function(eventExpr, # nolint: object_name.+ #' output$summary <- renderText({
|
||
| 390 | +281 |
- handlerExpr, # nolint: object_name.+ #' validate_has_variable(data, input$var) |
||
| 391 | +282 |
- event.env = parent.frame(), # nolint: object_name.+ #' paste0("Selected treatment variables: ", paste(input$var, collapse = ", "))
|
||
| 392 | +283 |
- handler.env = parent.frame(), # nolint: object_name.+ #' }) |
||
| 393 | +284 |
- ...) {
- |
- ||
| 394 | -178x - | -
- event_quo <- rlang::new_quosure(substitute(eventExpr), env = event.env)+ #' } |
||
| 395 | -178x - | +|||
| 285 | +
- handler_quo <- rlang::new_quosure(substitute(handlerExpr), env = handler.env)+ #' if (interactive()) {
|
|||
| 396 | +286 |
-
+ #' shinyApp(ui, server) |
||
| 397 | +287 |
- # When `condExpr` is TRUE, then `handlerExpr` is evaluated once.+ #' } |
||
| 398 | -178x - | +|||
| 288 | +
- activator <- reactive({
+ validate_has_variable <- function(data, varname, msg) {
|
|||
| 399 | -178x - | +|||
| 289 | +! |
- if (isTRUE(rlang::eval_tidy(event_quo))) {
+ if (length(varname) != 0) {
|
||
| 400 | -146x - | +|||
| 290 | +! |
- TRUE+ has_vars <- varname %in% names(data) |
||
| 401 | +291 |
- }+ |
||
| 402 | -+ | |||
| 292 | +! |
- })+ if (!all(has_vars)) {
|
||
| 403 | -+ | |||
| 293 | +! |
-
+ if (missing(msg)) {
|
||
| 404 | -178x - | +|||
| 294 | +! |
- observeEvent(+ msg <- sprintf( |
||
| 405 | -178x - | +|||
| 295 | +! |
- eventExpr = activator(),+ "%s does not have the required variables: %s.", |
||
| 406 | -178x - | +|||
| 296 | +! |
- once = TRUE,+ deparse(substitute(data)), |
||
| 407 | -178x - | +|||
| 297 | +! |
- handlerExpr = rlang::eval_tidy(handler_quo),+ toString(varname[!has_vars]) |
||
| 408 | +298 |
- ...+ ) |
||
| 409 | +299 |
- )+ } |
||
| 410 | -+ | |||
| 300 | +! |
- }+ validate(need(FALSE, msg)) |
| 1 | +301 |
- #' Get client timezone+ } |
|
| 2 | +302 |
- #'+ } |
|
| 3 | +303 |
- #' User timezone in the browser may be different to the one on the server.+ } |
|
| 4 | +304 |
- #' This script can be run to register a `shiny` input which contains information about the timezone in the browser.+ |
|
| 5 | +305 |
- #'+ #' Validate that variables has expected number of levels |
|
| 6 | +306 |
- #' @param ns (`function`) namespace function passed from the `session` object in the `shiny` server.+ #' |
|
| 7 | +307 |
- #' For `shiny` modules this will allow for proper name spacing of the registered input.+ #' `r lifecycle::badge("stable")`
|
|
| 8 | +308 |
#' |
|
| 9 | +309 |
- #' @return `NULL`, invisibly.+ #' If the number of levels of `x` is less than `min_levels` |
|
| 10 | +310 |
- #'+ #' or greater than `max_levels` the validation will fail. |
|
| 11 | +311 |
- #' @keywords internal+ #' This function is a wrapper for `shiny::validate`. |
|
| 12 | +312 |
#' |
|
| 13 | +313 |
- get_client_timezone <- function(ns) {
+ #' @param x variable name. If `x` is not a factor, the unique values |
|
| 14 | -78x - | +||
| 314 | +
- script <- sprintf(+ #' are treated as levels. |
||
| 15 | -78x - | +||
| 315 | +
- "Shiny.setInputValue(`%s`, Intl.DateTimeFormat().resolvedOptions().timeZone)",+ #' @param min_levels cutoff for minimum number of levels of `x` |
||
| 16 | -78x - | +||
| 316 | +
- ns("timezone")
+ #' @param max_levels cutoff for maximum number of levels of `x` |
||
| 17 | +317 |
- )+ #' @param var_name name of variable being validated for use in |
|
| 18 | -78x - | +||
| 318 | +
- shinyjs::runjs(script) # function does not return anything+ #' validation message |
||
| 19 | -78x - | +||
| 319 | +
- invisible(NULL)+ #' |
||
| 20 | +320 |
- }+ #' @export |
|
| 21 | +321 |
-
+ #' @examples |
|
| 22 | +322 |
- #' Resolve the expected bootstrap theme+ #' data <- data.frame( |
|
| 23 | +323 |
- #' @noRd+ #' one = rep("a", length.out = 20),
|
|
| 24 | +324 |
- #' @keywords internal+ #' two = rep(c("a", "b"), length.out = 20),
|
|
| 25 | +325 |
- get_teal_bs_theme <- function() {
+ #' three = rep(c("a", "b", "c"), length.out = 20),
|
|
| 26 | -4x - | +||
| 326 | +
- bs_theme <- getOption("teal.bs_theme")
+ #' four = rep(c("a", "b", "c", "d"), length.out = 20),
|
||
| 27 | +327 |
-
+ #' stringsAsFactors = TRUE |
|
| 28 | -4x - | +||
| 328 | +
- if (is.null(bs_theme)) {
+ #' ) |
||
| 29 | -1x - | +||
| 329 | +
- return(NULL)+ #' ui <- fluidPage( |
||
| 30 | +330 |
- }+ #' selectInput( |
|
| 31 | +331 |
-
+ #' "var", |
|
| 32 | -3x - | +||
| 332 | +
- if (!checkmate::test_class(bs_theme, "bs_theme")) {
+ #' "Select variable", |
||
| 33 | -2x - | +||
| 333 | +
- warning(+ #' choices = c("one", "two", "three", "four"),
|
||
| 34 | -2x - | +||
| 334 | +
- "Assertion on 'teal.bs_theme' option value failed: ",+ #' selected = "one" |
||
| 35 | -2x - | +||
| 335 | +
- checkmate::check_class(bs_theme, "bs_theme"),+ #' ), |
||
| 36 | -2x - | +||
| 336 | +
- ". The default Shiny Bootstrap theme will be used."+ #' verbatimTextOutput("summary")
|
||
| 37 | +337 |
- )+ #' ) |
|
| 38 | -2x - | +||
| 338 | +
- return(NULL)+ #' |
||
| 39 | +339 |
- }+ #' server <- function(input, output) {
|
|
| 40 | +340 |
-
+ #' output$summary <- renderText({
|
|
| 41 | -1x - | +||
| 341 | +
- bs_theme+ #' validate_n_levels(data[[input$var]], min_levels = 2, max_levels = 15, var_name = input$var) |
||
| 42 | +342 |
- }+ #' paste0( |
|
| 43 | +343 |
-
+ #' "Levels of selected treatment variable: ", |
|
| 44 | +344 |
- #' Return parentnames along with datanames.+ #' paste(levels(data[[input$var]]), |
|
| 45 | +345 |
- #' @noRd+ #' collapse = ", " |
|
| 46 | +346 |
- #' @keywords internal+ #' ) |
|
| 47 | +347 |
- .include_parent_datanames <- function(datanames, join_keys) {
- |
- |
| 48 | -157x - | -
- ordered_datanames <- datanames- |
- |
| 49 | -157x - | -
- for (i in datanames) {
- |
- |
| 50 | -275x - | -
- parents <- character(0)- |
- |
| 51 | -275x - | -
- while (length(i) > 0) {
- |
- |
| 52 | -288x - | -
- parent_i <- teal.data::parent(join_keys, i)- |
- |
| 53 | -288x - | -
- parents <- c(parent_i, parents)- |
- |
| 54 | -288x - | -
- i <- parent_i+ #' ) |
|
| 55 | +348 |
- }- |
- |
| 56 | -275x - | -
- ordered_datanames <- c(parents, ordered_datanames)+ #' }) |
|
| 57 | +349 |
- }- |
- |
| 58 | -157x - | -
- unique(ordered_datanames)+ #' } |
|
| 59 | +350 |
- }+ #' if (interactive()) {
|
|
| 60 | +351 |
-
+ #' shinyApp(ui, server) |
|
| 61 | +352 |
- #' Return topologicaly sorted datanames+ #' } |
|
| 62 | +353 |
- #' @noRd+ validate_n_levels <- function(x, min_levels = 1, max_levels = 12, var_name) {
|
|
| 63 | -+ | ||
| 354 | +! |
- #' @keywords internal+ x_levels <- if (is.factor(x)) {
|
|
| 64 | -+ | ||
| 355 | +! |
- .topologically_sort_datanames <- function(datanames, join_keys) {
+ levels(x) |
|
| 65 | -131x - | +||
| 356 | +
- datanames_with_parents <- .include_parent_datanames(datanames, join_keys)+ } else {
|
||
| 66 | -131x - | +||
| 357 | +! |
- intersect(datanames, datanames_with_parents)+ unique(x) |
|
| 67 | +358 |
- }+ } |
|
| 68 | +359 | ||
| 69 | -+ | ||
| 360 | +! |
- #' Create a `FilteredData`+ if (!is.null(min_levels) && !(is.null(max_levels))) {
|
|
| 70 | -+ | ||
| 361 | +! |
- #'+ validate(need( |
|
| 71 | -+ | ||
| 362 | +! |
- #' Create a `FilteredData` object from a `teal_data` object.+ length(x_levels) >= min_levels && length(x_levels) <= max_levels, |
|
| 72 | -+ | ||
| 363 | +! |
- #'+ sprintf( |
|
| 73 | -+ | ||
| 364 | +! |
- #' @param x (`teal_data`) object+ "%s variable needs minimum %s level(s) and maximum %s level(s).", |
|
| 74 | -+ | ||
| 365 | +! |
- #' @param datanames (`character`) vector of data set names to include; must be subset of `datanames(x)`+ var_name, min_levels, max_levels |
|
| 75 | +366 |
- #' @return A `FilteredData` object.+ ) |
|
| 76 | +367 |
- #' @keywords internal+ )) |
|
| 77 | -+ | ||
| 368 | +! |
- teal_data_to_filtered_data <- function(x, datanames = ls(teal.code::get_env(x))) {
+ } else if (!is.null(min_levels)) {
|
|
| 78 | -73x - | +||
| 369 | +! |
- checkmate::assert_class(x, "teal_data")+ validate(need( |
|
| 79 | -73x - | +||
| 370 | +! |
- checkmate::assert_character(datanames, min.chars = 1L, any.missing = FALSE)+ length(x_levels) >= min_levels,+ |
+ |
| 371 | +! | +
+ sprintf("%s variable needs minimum %s levels(s)", var_name, min_levels)
|
|
| 80 | +372 |
- # Otherwise, FilteredData will be created in the modules' scope later+ )) |
|
| 81 | -73x - | +||
| 373 | +! |
- teal.slice::init_filtered_data(+ } else if (!is.null(max_levels)) {
|
|
| 82 | -73x - | +||
| 374 | +! |
- x = Filter(+ validate(need( |
|
| 83 | -73x - | +||
| 375 | +! |
- length,+ length(x_levels) <= max_levels, |
|
| 84 | -73x - | +||
| 376 | +! |
- sapply(datanames, function(dn) x[[dn]], simplify = FALSE)+ sprintf("%s variable needs maximum %s level(s)", var_name, max_levels)
|
|
| 85 | +377 |
- ),- |
- |
| 86 | -73x - | -
- join_keys = teal.data::join_keys(x)+ )) |
|
| 87 | +378 |
- )+ } |
|
| 88 | +379 |
} |
| 89 | +1 |
-
+ #' Module to transform `reactive` `teal_data` |
||
| 90 | +2 |
-
+ #' |
||
| 91 | +3 |
- #' Template function for `TealReportCard` creation and customization+ #' Module calls multiple [`module_teal_data`] in sequence so that `reactive teal_data` output |
||
| 92 | +4 |
- #'+ #' from one module is handed over to the following module's input. |
||
| 93 | +5 |
- #' This function generates a report card with a title,+ #' |
||
| 94 | +6 |
- #' an optional description, and the option to append the filter state list.+ #' @inheritParams module_teal_data |
||
| 95 | +7 |
- #'+ #' @inheritParams teal_modules |
||
| 96 | +8 |
- #' @param title (`character(1)`) title of the card (unless overwritten by label)+ #' @return `reactive` `teal_data` |
||
| 97 | +9 |
- #' @param label (`character(1)`) label provided by the user when adding the card+ #' |
||
| 98 | +10 |
- #' @param description (`character(1)`) optional, additional description+ #' |
||
| 99 | +11 |
- #' @param with_filter (`logical(1)`) flag indicating to add filter state+ #' @name module_transform_data |
||
| 100 | +12 |
- #' @param filter_panel_api (`FilterPanelAPI`) object with API that allows the generation+ #' @keywords internal |
||
| 101 | +13 |
- #' of the filter state in the report+ NULL |
||
| 102 | +14 |
- #'+ |
||
| 103 | +15 |
- #' @return (`TealReportCard`) populated with a title, description and filter state.+ #' @rdname module_transform_data |
||
| 104 | +16 |
- #'+ ui_transform_data <- function(id, transformers = list(), class = "well") {
|
||
| 105 | -+ | |||
| 17 | +! |
- #' @export+ checkmate::assert_string(id) |
||
| 106 | -+ | |||
| 18 | +! |
- report_card_template <- function(title, label, description = NULL, with_filter, filter_panel_api) {
+ checkmate::assert_list(transformers, "teal_transform_module") |
||
| 107 | -2x - | +|||
| 19 | +
- checkmate::assert_string(title)+ |
|||
| 108 | -2x - | +|||
| 20 | +! |
- checkmate::assert_string(label)+ ns <- NS(id) |
||
| 109 | -2x - | +|||
| 21 | +! |
- checkmate::assert_string(description, null.ok = TRUE)+ labels <- lapply(transformers, function(x) attr(x, "label")) |
||
| 110 | -2x - | +|||
| 22 | +! |
- checkmate::assert_flag(with_filter)+ ids <- get_unique_labels(labels) |
||
| 111 | -2x - | +|||
| 23 | +! |
- checkmate::assert_class(filter_panel_api, classes = "FilterPanelAPI")+ names(transformers) <- ids |
||
| 112 | +24 | |||
| 113 | -2x - | -
- card <- teal::TealReportCard$new()- |
- ||
| 114 | -2x - | +|||
| 25 | +! |
- title <- if (label == "") title else label+ lapply( |
||
| 115 | -2x - | +|||
| 26 | +! |
- card$set_name(title)+ names(transformers), |
||
| 116 | -2x - | +|||
| 27 | +! |
- card$append_text(title, "header2")+ function(name) {
|
||
| 117 | -1x - | +|||
| 28 | +! |
- if (!is.null(description)) card$append_text(description, "header3")+ data_mod <- transformers[[name]] |
||
| 118 | -1x - | +|||
| 29 | +! |
- if (with_filter) card$append_fs(filter_panel_api$get_filter_state())+ wrapper_id <- ns(sprintf("wrapper_%s", name))
|
||
| 119 | -2x - | +|||
| 30 | +! |
- card+ div( # todo: accordion? |
||
| 120 | +31 |
- }+ # class .teal_validated changes the color of the boarder on error in ui_validate_reactive_teal_data |
||
| 121 | +32 |
-
+ # For details see tealValidate.js file. |
||
| 122 | -+ | |||
| 33 | +! |
-
+ class = c(class, "teal_validated"), |
||
| 123 | -+ | |||
| 34 | +! |
- #' Check `datanames` in modules+ title = attr(data_mod, "label"), |
||
| 124 | -+ | |||
| 35 | +! |
- #'+ tags$span( |
||
| 125 | -+ | |||
| 36 | +! |
- #' This function ensures specified `datanames` in modules match those in the data object,+ class = "text-primary mb-4", |
||
| 126 | -+ | |||
| 37 | +! |
- #' returning error messages or `TRUE` for successful validation.+ icon("fas fa-square-pen"),
|
||
| 127 | -+ | |||
| 38 | +! |
- #'+ attr(data_mod, "label") |
||
| 128 | +39 |
- #' @param modules (`teal_modules`) object+ ), |
||
| 129 | -+ | |||
| 40 | +! |
- #' @param datanames (`character`) names of datasets available in the `data` object+ tags$i( |
||
| 130 | -+ | |||
| 41 | +! |
- #'+ class = "remove pull-right fa fa-angle-down", |
||
| 131 | -- |
- #' @return A `character(1)` containing error message or `TRUE` if validation passes.- |
- ||
| 132 | -- |
- #' @keywords internal- |
- ||
| 133 | -- |
- check_modules_datanames <- function(modules, datanames) {
- |
- ||
| 134 | -166x - | -
- checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"))
- |
- ||
| 135 | -166x - | +|||
| 42 | +! |
- checkmate::assert_character(datanames)+ style = "cursor: pointer;", |
||
| 136 | -+ | |||
| 43 | +! |
-
+ title = "fold/expand transform panel", |
||
| 137 | -166x - | +|||
| 44 | +! |
- recursive_check_datanames <- function(modules, datanames) {
+ onclick = sprintf("togglePanelItems(this, '%s', 'fa-angle-right', 'fa-angle-down');", wrapper_id)
|
||
| 138 | +45 |
- # check teal_modules against datanames- |
- ||
| 139 | -259x - | -
- if (inherits(modules, "teal_modules")) {
- |
- ||
| 140 | -73x - | -
- result <- lapply(modules$children, function(module) recursive_check_datanames(module, datanames = datanames))+ ), |
||
| 141 | -73x - | +|||
| 46 | +! |
- result <- result[vapply(result, Negate(is.null), logical(1L))]+ div( |
||
| 142 | -73x - | +|||
| 47 | +! |
- if (length(result) == 0) {
+ id = wrapper_id, |
||
| 143 | -65x - | +|||
| 48 | +! |
- return(NULL)+ ui_teal_data(id = ns(name), data_module = transformers[[name]]$ui) |
||
| 144 | +49 |
- }- |
- ||
| 145 | -8x - | -
- list(- |
- ||
| 146 | -8x - | -
- string = do.call(c, as.list(unname(sapply(result, function(x) x$string)))),- |
- ||
| 147 | -8x - | -
- html = function(with_module_name = TRUE) {
- |
- ||
| 148 | -6x - | -
- tagList(- |
- ||
| 149 | -6x - | -
- lapply(+ ) |
||
| 150 | -6x - | +|||
| 50 | +
- result,+ ) |
|||
| 151 | -6x - | +|||
| 51 | +
- function(x) x$html(with_module_name = with_module_name)+ } |
|||
| 152 | +52 |
- )+ ) |
||
| 153 | +53 |
- )+ } |
||
| 154 | +54 |
- }+ |
||
| 155 | +55 |
- )+ #' @rdname module_transform_data |
||
| 156 | +56 |
- } else {
+ srv_transform_data <- function(id, data, transformers = list(), modules, is_transformer_failed = reactiveValues()) {
|
||
| 157 | -186x - | +57 | +79x |
- extra_datanames <- setdiff(modules$datanames, c("all", datanames))
+ checkmate::assert_string(id) |
| 158 | -186x - | +58 | +79x |
- if (length(extra_datanames)) {
+ assert_reactive(data) |
| 159 | -11x - | +59 | +79x |
- list(+ checkmate::assert_list(transformers, "teal_transform_module") |
| 160 | -11x - | +60 | +79x |
- string = build_datanames_error_message(+ checkmate::assert_class(modules, "teal_module") |
| 161 | -11x - | +61 | +79x |
- modules$label,+ labels <- lapply(transformers, function(x) attr(x, "label")) |
| 162 | -11x - | +62 | +79x |
- datanames,+ ids <- get_unique_labels(labels) |
| 163 | -11x - | +63 | +79x |
- extra_datanames,+ names(transformers) <- ids |
| 164 | -11x - | +64 | +79x |
- tags = list(+ moduleServer(id, function(input, output, session) {
|
| 165 | -11x - | +65 | +79x |
- span = function(..., .noWS = NULL) { # nolint: object_name
+ logger::log_debug("srv_teal_data_modules initializing.")
|
| 166 | -78x - | -
- trimws(paste(..., sep = ifelse(is.null(.noWS), " ", ""), collapse = " "))- |
- ||
| 167 | -+ | 66 | +79x |
- },+ Reduce( |
| 168 | -11x - | -
- code = function(x) toString(dQuote(x, q = FALSE))- |
- ||
| 169 | -+ | 67 | +79x |
- ),+ function(previous_result, name) {
|
| 170 | -11x - | +68 | +19x |
- tagList = function(...) trimws(paste(...))+ srv_teal_data( |
| 171 | -+ | |||
| 69 | +19x |
- ),+ id = name, |
||
| 172 | -+ | |||
| 70 | +19x |
- # Build HTML representation of the error message with <pre> formatting+ data_module = function(id) transformers[[name]]$server(id, previous_result), |
||
| 173 | -11x - | +71 | +19x |
- html = function(with_module_name = TRUE) {
+ modules = modules, |
| 174 | -9x - | +72 | +19x |
- tagList(+ is_transformer_failed = is_transformer_failed |
| 175 | -9x - | +|||
| 73 | +
- build_datanames_error_message(+ ) |
|||
| 176 | -9x - | +|||
| 74 | +
- if (with_module_name) modules$label,+ }, |
|||
| 177 | -9x - | +75 | +79x |
- datanames,+ x = names(transformers), |
| 178 | -9x - | +76 | +79x |
- extra_datanames+ init = data |
| 179 | +77 |
- ),- |
- ||
| 180 | -9x - | -
- tags$br(.noWS = "before")+ ) |
||
| 181 | +78 |
- )+ }) |
||
| 182 | +79 |
- }+ } |
| 183 | +1 |
- )+ #' Manage multiple `FilteredData` objects |
||
| 184 | +2 |
- }+ #' |
||
| 185 | +3 |
- }+ #' @description |
||
| 186 | +4 |
- }+ #' Oversee filter states across the entire application. |
||
| 187 | -166x - | +|||
| 5 | +
- check_datanames <- recursive_check_datanames(modules, datanames)+ #' |
|||
| 188 | -166x - | +|||
| 6 | +
- if (length(check_datanames)) {
+ #' @section Slices global: |
|||
| 189 | -11x - | +|||
| 7 | +
- check_datanames+ #' The key role in maintaining the module-specific filter states is played by the `.slicesGlobal` |
|||
| 190 | +8 |
- } else {
+ #' object. It is a reference class that holds the following fields: |
||
| 191 | -155x - | +|||
| 9 | +
- TRUE+ #' - `all_slices` (`reactiveVal`) - reactive value containing all filters registered in an app. |
|||
| 192 | +10 |
- }+ #' - `module_slices_api` (`reactiveValues`) - reactive field containing references to each modules' |
||
| 193 | +11 |
- }+ #' `FilteredData` object methods. At this moment it is used only in `srv_filter_manager` to display |
||
| 194 | +12 |
-
+ #' the filter states in a table combining informations from `all_slices` and from |
||
| 195 | +13 |
- #' Check `datanames` in filters+ #' `FilteredData$get_available_teal_slices()`. |
||
| 196 | +14 |
#' |
||
| 197 | +15 |
- #' This function checks whether `datanames` in filters correspond to those in `data`,+ #' During a session only new filters are added to `all_slices` unless [`module_snapshot_manager`] is |
||
| 198 | +16 |
- #' returning character vector with error messages or `TRUE` if all checks pass.+ #' used to restore previous state. Filters from `all_slices` can be activated or deactivated in a |
||
| 199 | +17 |
- #'+ #' module which is linked (both ways) by `attr(, "mapping")` so that: |
||
| 200 | +18 |
- #' @param filters (`teal_slices`) object+ #' - If module's filter is added or removed in its `FilteredData` object, this information is passed |
||
| 201 | +19 |
- #' @param datanames (`character`) names of datasets available in the `data` object+ #' to `SlicesGlobal` which updates `attr(, "mapping")` accordingly. |
||
| 202 | +20 |
- #'+ #' - When mapping changes in a `SlicesGlobal`, filters are set or removed from module's |
||
| 203 | +21 |
- #' @return A `character(1)` containing error message or TRUE if validation passes.+ #' `FilteredData`. |
||
| 204 | +22 |
- #' @keywords internal+ #' |
||
| 205 | +23 |
- check_filter_datanames <- function(filters, datanames) {
+ #' @section Filter manager: |
||
| 206 | -73x - | +|||
| 24 | +
- checkmate::assert_class(filters, "teal_slices")+ #' Filter-manager is split into two parts: |
|||
| 207 | -73x - | +|||
| 25 | +
- checkmate::assert_character(datanames)+ #' 1. `ui/srv_filter_manager_panel` - Called once for the whole app. This module observes changes in |
|||
| 208 | +26 |
-
+ #' the filters in `slices_global` and displays them in a table utilizing information from `mapping`: |
||
| 209 | +27 |
- # check teal_slices against datanames+ #' - (`TRUE`) - filter is active in the module |
||
| 210 | -73x - | +|||
| 28 | +
- out <- unlist(sapply(+ #' - (`FALSE`) - filter is inactive in the module |
|||
| 211 | -73x - | +|||
| 29 | +
- filters, function(filter) {
+ #' - (`NA`) - filter is not available in the module |
|||
| 212 | -24x - | +|||
| 30 | +
- dataname <- shiny::isolate(filter$dataname)+ #' 2. `ui/srv_module_filter_manager` - Called once for each `teal_module`. Handling filter states |
|||
| 213 | -24x - | +|||
| 31 | +
- if (!dataname %in% datanames) {
+ #' for of single module and keeping module `FilteredData` consistent with `slices_global`, so that |
|||
| 214 | -3x - | +|||
| 32 | +
- sprintf(+ #' local filters are always reflected in the `slices_global` and its mapping and vice versa. |
|||
| 215 | -3x - | +|||
| 33 | +
- "- Filter '%s' refers to dataname not available in 'data':\n %s not in (%s)",+ #' |
|||
| 216 | -3x - | +|||
| 34 | +
- shiny::isolate(filter$id),+ #' |
|||
| 217 | -3x - | +|||
| 35 | +
- dQuote(dataname, q = FALSE),+ #' @param id (`character(1)`) |
|||
| 218 | -3x - | +|||
| 36 | +
- toString(dQuote(datanames, q = FALSE))+ #' `shiny` module instance id. |
|||
| 219 | +37 |
- )+ #' |
||
| 220 | +38 |
- }+ #' @param slices_global (`reactiveVal`) |
||
| 221 | +39 |
- }+ #' containing `teal_slices`. |
||
| 222 | +40 |
- ))+ #' |
||
| 223 | +41 |
-
+ #' @param module_fd (`FilteredData`) |
||
| 224 | +42 |
-
+ #' Object containing the data to be filtered in a single `teal` module. |
||
| 225 | -73x - | +|||
| 43 | +
- if (length(out)) {
+ #' |
|||
| 226 | -3x - | +|||
| 44 | +
- paste(out, collapse = "\n")+ #' @return |
|||
| 227 | +45 |
- } else {
+ #' Module returns a `slices_global` (`reactiveVal`) containing a `teal_slices` object with mapping. |
||
| 228 | -70x - | +|||
| 46 | +
- TRUE+ #' |
|||
| 229 | +47 |
- }+ #' @encoding UTF-8 |
||
| 230 | +48 |
- }+ #' |
||
| 231 | +49 |
-
+ #' @name module_filter_manager |
||
| 232 | +50 |
- #' Function for validating the title parameter of `teal::init`+ #' @rdname module_filter_manager |
||
| 233 | +51 |
#' |
||
| 234 | +52 |
- #' Checks if the input of the title from `teal::init` will create a valid title and favicon tag.+ NULL |
||
| 235 | +53 |
- #' @param shiny_tag (`shiny.tag`) Object to validate for a valid title.+ |
||
| 236 | +54 |
- #' @keywords internal+ #' @rdname module_filter_manager |
||
| 237 | +55 |
- validate_app_title_tag <- function(shiny_tag) {
- |
- ||
| 238 | -7x - | -
- checkmate::assert_class(shiny_tag, "shiny.tag")- |
- ||
| 239 | -7x - | -
- checkmate::assert_true(shiny_tag$name == "head")- |
- ||
| 240 | -6x - | -
- child_names <- vapply(shiny_tag$children, `[[`, character(1L), "name")- |
- ||
| 241 | -6x - | -
- checkmate::assert_subset(c("title", "link"), child_names, .var.name = "child tags")
+ ui_filter_manager_panel <- function(id) {
|
||
| 242 | -4x - | +|||
| 56 | +! |
- rel_attr <- shiny_tag$children[[which(child_names == "link")]]$attribs$rel+ ns <- NS(id) |
||
| 243 | -4x - | +|||
| 57 | +! |
- checkmate::assert_subset(+ tags$button( |
||
| 244 | -4x - | +|||
| 58 | +! |
- rel_attr,+ id = ns("show_filter_manager"),
|
||
| 245 | -4x - | +|||
| 59 | +! |
- c("icon", "shortcut icon"),
+ class = "btn action-button wunder_bar_button", |
||
| 246 | -4x - | +|||
| 60 | +! |
- .var.name = "Link tag's rel attribute",+ title = "View filter mapping", |
||
| 247 | -4x - | +|||
| 61 | +! |
- empty.ok = FALSE+ suppressMessages(icon("fas fa-grip"))
|
||
| 248 | +62 |
) |
||
| 249 | +63 |
} |
||
| 250 | +64 | |||
| 251 | -- |
- #' Build app title with favicon- |
- ||
| 252 | -- |
- #'- |
- ||
| 253 | -- |
- #' A helper function to create the browser title along with a logo.- |
- ||
| 254 | -- |
- #'- |
- ||
| 255 | -- |
- #' @param title (`character`) The browser title for the `teal` app.- |
- ||
| 256 | +65 |
- #' @param favicon (`character`) The path for the icon for the title.+ #' @rdname module_filter_manager |
||
| 257 | +66 |
- #' The image/icon path can be remote or the static path accessible by `shiny`, like the `www/`+ #' @keywords internal |
||
| 258 | +67 |
- #'+ srv_filter_manager_panel <- function(id, slices_global) {
|
||
| 259 | -+ | |||
| 68 | +80x |
- #' @return A `shiny.tag` containing the element that adds the title and logo to the `shiny` app.+ checkmate::assert_string(id) |
||
| 260 | -+ | |||
| 69 | +80x |
- #' @export+ checkmate::assert_class(slices_global, ".slicesGlobal") |
||
| 261 | -+ | |||
| 70 | +80x |
- build_app_title <- function(+ moduleServer(id, function(input, output, session) {
|
||
| 262 | -+ | |||
| 71 | +80x |
- title = "teal app",+ setBookmarkExclude(c("show_filter_manager"))
|
||
| 263 | -+ | |||
| 72 | +80x |
- favicon = "https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/PNG/nest.png") {
+ observeEvent(input$show_filter_manager, {
|
||
| 264 | -12x - | +|||
| 73 | +! |
- checkmate::assert_string(title, null.ok = TRUE)+ logger::log_debug("srv_filter_manager_panel@1 show_filter_manager button has been clicked.")
|
||
| 265 | -12x - | +|||
| 74 | +! |
- checkmate::assert_string(favicon, null.ok = TRUE)+ showModal( |
||
| 266 | -12x - | +|||
| 75 | +! |
- tags$head(+ modalDialog( |
||
| 267 | -12x - | +|||
| 76 | +! |
- tags$title(title),+ ui_filter_manager(session$ns("filter_manager")),
|
||
| 268 | -12x - | +|||
| 77 | +! |
- tags$link(+ class = "filter_manager_modal", |
||
| 269 | -12x - | +|||
| 78 | +! |
- rel = "icon",+ size = "l", |
||
| 270 | -12x - | +|||
| 79 | +! |
- href = favicon,+ footer = NULL, |
||
| 271 | -12x - | +|||
| 80 | +! |
- sizes = "any"+ easyClose = TRUE |
||
| 272 | +81 |
- )+ ) |
||
| 273 | +82 |
- )+ ) |
||
| 274 | +83 |
- }+ }) |
||
| 275 | -+ | |||
| 84 | +80x |
-
+ srv_filter_manager("filter_manager", slices_global = slices_global)
|
||
| 276 | +85 |
- #' Application ID+ }) |
||
| 277 | +86 |
- #'+ } |
||
| 278 | +87 |
- #' Creates App ID used to match filter snapshots to application.+ |
||
| 279 | +88 |
- #'+ #' @rdname module_filter_manager |
||
| 280 | +89 |
- #' Calculate app ID that will be used to stamp filter state snapshots.+ ui_filter_manager <- function(id) {
|
||
| 281 | -+ | |||
| 90 | +! |
- #' App ID is a hash of the app's data and modules.+ ns <- NS(id) |
||
| 282 | -+ | |||
| 91 | +! |
- #' See "transferring snapshots" section in ?snapshot.+ actionButton(ns("filter_manager"), NULL, icon = icon("fas fa-filter"))
|
||
| 283 | -+ | |||
| 92 | +! |
- #'+ tags$div( |
||
| 284 | -+ | |||
| 93 | +! |
- #' @param data (`teal_data` or `teal_data_module`) as accepted by `init`+ class = "filter_manager_content", |
||
| 285 | -+ | |||
| 94 | +! |
- #' @param modules (`teal_modules`) object as accepted by `init`+ tableOutput(ns("slices_table"))
|
||
| 286 | +95 |
- #'+ ) |
||
| 287 | +96 |
- #' @return A single character string.+ } |
||
| 288 | +97 |
- #'+ |
||
| 289 | +98 |
- #' @keywords internal+ #' @rdname module_filter_manager |
||
| 290 | +99 |
- create_app_id <- function(data, modules) {
+ srv_filter_manager <- function(id, slices_global) {
|
||
| 291 | -20x - | +100 | +80x |
- checkmate::assert_multi_class(data, c("teal_data", "teal_data_module"))
+ checkmate::assert_string(id) |
| 292 | -19x - | +101 | +80x |
- checkmate::assert_class(modules, "teal_modules")+ checkmate::assert_class(slices_global, ".slicesGlobal") |
| 293 | +102 | |||
| 294 | -18x - | -
- data <- if (inherits(data, "teal_data")) {
- |
- ||
| 295 | -16x - | +103 | +80x |
- as.list(teal.code::get_env(data))+ moduleServer(id, function(input, output, session) {
|
| 296 | -18x - | +104 | +80x |
- } else if (inherits(data, "teal_data_module")) {
+ logger::log_debug("filter_manager_srv initializing.")
|
| 297 | -2x - | +|||
| 105 | +
- deparse1(body(data$server))+ |
|||
| 298 | +106 |
- }+ # Bookmark slices global with mapping. |
||
| 299 | -18x - | +107 | +80x |
- modules <- lapply(modules, defunction)+ session$onBookmark(function(state) {
|
| 300 | -+ | |||
| 108 | +! |
-
+ logger::log_debug("filter_manager_srv@onBookmark: storing filter state")
|
||
| 301 | -18x - | +|||
| 109 | +! |
- rlang::hash(list(data = data, modules = modules))+ state$values$filter_state_on_bookmark <- as.list( |
||
| 302 | -+ | |||
| 110 | +! |
- }+ slices_global$all_slices(), |
||
| 303 | -+ | |||
| 111 | +! |
-
+ recursive = TRUE |
||
| 304 | +112 |
- #' Go through list and extract bodies of encountered functions as string, recursively.+ ) |
||
| 305 | +113 |
- #' @keywords internal+ }) |
||
| 306 | +114 |
- #' @noRd+ |
||
| 307 | -+ | |||
| 115 | +80x |
- defunction <- function(x) {
+ bookmarked_slices <- restoreValue(session$ns("filter_state_on_bookmark"), NULL)
|
||
| 308 | -219x - | +116 | +80x |
- if (is.list(x)) {
+ if (!is.null(bookmarked_slices)) {
|
| 309 | -64x - | +|||
| 117 | +! |
- lapply(x, defunction)+ logger::log_debug("filter_manager_srv: restoring filter state from bookmark.")
|
||
| 310 | -155x - | +|||
| 118 | +! |
- } else if (is.function(x)) {
+ slices_global$slices_set(bookmarked_slices) |
||
| 311 | -48x - | +|||
| 119 | +
- deparse1(body(x))+ } |
|||
| 312 | +120 |
- } else {
+
|
||
| 313 | -107x - | +121 | +80x |
- x+ mapping_table <- reactive({
|
| 314 | +122 |
- }+ # We want this to be reactive on slices_global$all_slices() only as get_available_teal_slices() |
||
| 315 | +123 |
- }+ # is dependent on slices_global$all_slices(). |
||
| 316 | -+ | |||
| 124 | +89x |
-
+ module_labels <- setdiff( |
||
| 317 | -+ | |||
| 125 | +89x |
- #' Get unique labels+ names(attr(slices_global$all_slices(), "mapping")), |
||
| 318 | -+ | |||
| 126 | +89x |
- #'+ "Report previewer" |
||
| 319 | +127 |
- #' Get unique labels for the modules to avoid namespace conflicts.+ ) |
||
| 320 | -+ | |||
| 128 | +89x |
- #'+ isolate({
|
||
| 321 | -+ | |||
| 129 | +89x |
- #' @param labels (`character`) vector of labels+ mm <- as.data.frame( |
||
| 322 | -+ | |||
| 130 | +89x |
- #'+ sapply( |
||
| 323 | -+ | |||
| 131 | +89x |
- #' @return (`character`) vector of unique labels+ module_labels, |
||
| 324 | -+ | |||
| 132 | +89x |
- #'+ simplify = FALSE, |
||
| 325 | -+ | |||
| 133 | +89x |
- #' @keywords internal+ function(module_label) {
|
||
| 326 | -+ | |||
| 134 | +102x |
- get_unique_labels <- function(labels) {
+ available_slices <- slices_global$module_slices_api[[module_label]]$get_available_teal_slices() |
||
| 327 | -204x - | +135 | +94x |
- make.unique(gsub("[^[:alnum:]]", "_", tolower(labels)), sep = "_")
+ global_ids <- sapply(slices_global$all_slices(), `[[`, "id", simplify = FALSE) |
| 328 | -+ | |||
| 136 | +94x |
- }+ module_ids <- sapply(slices_global$slices_get(module_label), `[[`, "id", simplify = FALSE) |
||
| 329 | -+ | |||
| 137 | +94x |
-
+ allowed_ids <- vapply(available_slices, `[[`, character(1L), "id") |
||
| 330 | -+ | |||
| 138 | +94x |
- #' Remove ANSI escape sequences from a string+ active_ids <- global_ids %in% module_ids |
||
| 331 | -+ | |||
| 139 | +94x |
- #' @noRd+ setNames(nm = global_ids, ifelse(global_ids %in% allowed_ids, active_ids, NA)) |
||
| 332 | +140 |
- strip_style <- function(string) {
- |
- ||
| 333 | -2x - | -
- checkmate::assert_string(string)+ } |
||
| 334 | +141 | - - | -||
| 335 | -2x - | -
- gsub(+ ), |
||
| 336 | -2x - | +142 | +89x |
- "(?:(?:\\x{001b}\\[)|\\x{009b})(?:(?:[0-9]{1,3})?(?:(?:;[0-9]{0,3})*)?[A-M|f-m])|\\x{001b}[A-M]",
+ check.names = FALSE |
| 337 | +143 |
- "",+ ) |
||
| 338 | -2x - | +144 | +81x |
- string,+ colnames(mm)[colnames(mm) == "global_filters"] <- "Global filters" |
| 339 | -2x - | +|||
| 145 | +
- perl = TRUE,+ |
|||
| 340 | -2x - | +146 | +81x |
- useBytes = TRUE+ mm |
| 341 | +147 |
- )+ }) |
||
| 342 | +148 |
- }+ }) |
||
| 343 | +149 | |||
| 344 | -+ | |||
| 150 | +80x |
- #' Convert character list to human readable html with commas and "and"+ output$slices_table <- renderTable( |
||
| 345 | -+ | |||
| 151 | +80x |
- #' @noRd+ expr = {
|
||
| 346 | -+ | |||
| 152 | +89x |
- paste_datanames_character <- function(x,+ logger::log_debug("filter_manager_srv@1 rendering slices_table.")
|
||
| 347 | -+ | |||
| 153 | +89x |
- tags = list(span = shiny::tags$span, code = shiny::tags$code),+ mm <- mapping_table() |
||
| 348 | +154 |
- tagList = shiny::tagList) { # nolint: object_name.
+
|
||
| 349 | -38x - | +|||
| 155 | +
- checkmate::assert_character(x)+ # Display logical values as UTF characters. |
|||
| 350 | -38x - | +156 | +81x |
- do.call(+ mm[] <- lapply(mm, ifelse, yes = intToUtf8(9989), no = intToUtf8(10060)) |
| 351 | -38x - | +157 | +81x |
- tagList,+ mm[] <- lapply(mm, function(x) ifelse(is.na(x), intToUtf8(128306), x)) |
| 352 | -38x - | +|||
| 158 | +
- lapply(seq_along(x), function(.ix) {
+
|
|||
| 353 | -46x - | +|||
| 159 | +
- tagList(+ # Display placeholder if no filters defined. |
|||
| 354 | -46x - | +160 | +81x |
- tags$code(x[.ix]),+ if (nrow(mm) == 0L) {
|
| 355 | -46x - | +161 | +57x |
- if (.ix != length(x)) {
+ mm <- data.frame(`Filter manager` = "No filters specified.", check.names = FALSE) |
| 356 | -8x - | +162 | +57x |
- tags$span(ifelse(.ix == length(x) - 1, " and ", ", "))+ rownames(mm) <- "" |
| 357 | +163 |
} |
||
| 358 | -+ | |||
| 164 | +81x |
- )+ mm |
||
| 359 | +165 |
- })+ }, |
||
| 360 | -+ | |||
| 166 | +80x |
- )+ rownames = TRUE |
||
| 361 | +167 |
- }+ ) |
||
| 362 | +168 | |||
| 363 | -+ | |||
| 169 | +80x |
- #' Build datanames error string for error message+ mapping_table # for testing purpose |
||
| 364 | +170 |
- #'+ }) |
||
| 365 | +171 |
- #' tags and tagList are overwritten in arguments allowing to create strings for+ } |
||
| 366 | +172 |
- #' logging purposes+ |
||
| 367 | +173 |
- #' @noRd+ #' @rdname module_filter_manager |
||
| 368 | +174 |
- build_datanames_error_message <- function(label = NULL,+ srv_module_filter_manager <- function(id, module_fd, slices_global) {
|
||
| 369 | -+ | |||
| 175 | +105x |
- datanames,+ checkmate::assert_string(id) |
||
| 370 | -+ | |||
| 176 | +105x |
- extra_datanames,+ assert_reactive(module_fd) |
||
| 371 | -+ | |||
| 177 | +105x |
- tags = list(span = shiny::tags$span, code = shiny::tags$code),+ checkmate::assert_class(slices_global, ".slicesGlobal") |
||
| 372 | +178 |
- tagList = shiny::tagList) { # nolint: object_name.
+
|
||
| 373 | -20x - | +179 | +105x |
- tags$span(+ moduleServer(id, function(input, output, session) {
|
| 374 | -20x - | +180 | +105x |
- tags$span(ifelse(length(extra_datanames) > 1, "Datasets", "Dataset")),+ logger::log_debug("srv_module_filter_manager initializing for module: { id }.")
|
| 375 | -20x - | +|||
| 181 | +
- paste_datanames_character(extra_datanames, tags, tagList),+ # Track filter global and local states. |
|||
| 376 | -20x - | +182 | +105x |
- tags$span(+ slices_global_module <- reactive({
|
| 377 | -20x - | +183 | +189x | +
+ slices_global$slices_get(module_label = id)+ |
+
| 184 | +
- paste0(+ }) |
|||
| 378 | -20x - | +185 | +105x | +
+ slices_module <- reactive(req(module_fd())$get_filter_state())+ |
+
| 186 | +
- ifelse(length(extra_datanames) > 1, "are missing", "is missing"),+ |
|||
| 379 | -20x - | +187 | +105x |
- ifelse(is.null(label), ".", sprintf(" for tab '%s'.", label))
+ module_fd_previous <- reactiveVal(NULL) |
| 380 | +188 |
- )+ |
||
| 381 | +189 |
- ),+ # Set (reactively) available filters for the module. |
||
| 382 | -20x - | +190 | +105x |
- if (length(datanames) >= 1) {
+ obs1 <- observeEvent(module_fd(), priority = 1, {
|
| 383 | -18x - | +191 | +86x |
- tagList(+ logger::log_debug("srv_module_filter_manager@1 setting initial slices for module: { id }.")
|
| 384 | -18x - | +|||
| 192 | +
- tags$span(ifelse(length(datanames) > 1, "Datasets", "Dataset")),+ # Filters relevant for the module in module-specific app. |
|||
| 385 | -18x - | +193 | +86x |
- tags$span("available in data:"),
+ slices <- slices_global_module() |
| 386 | -18x - | +|||
| 194 | +
- tagList(+ |
|||
| 387 | -18x - | +|||
| 195 | +
- tags$span(+ # Clean up previous filter states and refresh cache of previous module_fd with current |
|||
| 388 | -18x - | +196 | +3x |
- paste_datanames_character(datanames, tags, tagList),+ if (!is.null(module_fd_previous())) module_fd_previous()$finalize() |
| 389 | -18x - | +197 | +86x |
- tags$span(".", .noWS = "outside"),
+ module_fd_previous(module_fd()) |
| 390 | -18x - | +|||
| 198 | +
- .noWS = c("outside")
+
|
|||
| 391 | +199 |
- )+ # Setting filter states from slices_global: |
||
| 392 | +200 |
- )+ # 1. when app initializes slices_global set to initial filters (specified by app developer) |
||
| 393 | +201 |
- )+ # 2. when data reinitializes slices_global reflects latest filter states |
||
| 394 | +202 |
- } else {
+
|
||
| 395 | -2x - | +203 | +86x |
- tags$span("No datasets are available in data.")
+ module_fd()$set_filter_state(slices) |
| 396 | +204 |
- }+ |
||
| 397 | +205 |
- )+ # irrelevant filters are discarded in FilteredData$set_available_teal_slices |
||
| 398 | +206 |
- }+ # it means we don't need to subset slices_global$all_slices() from filters refering to irrelevant datasets |
| 1 | -+ | |||
| 207 | +86x |
- #' `teal` main module+ module_fd()$set_available_teal_slices(slices_global$all_slices) |
||
| 2 | +208 |
- #'+ |
||
| 3 | +209 |
- #' @description+ # this needed in filter_manager_srv |
||
| 4 | -+ | |||
| 210 | +86x |
- #' `r lifecycle::badge("stable")`
+ slices_global$module_slices_api_set( |
||
| 5 | -+ | |||
| 211 | +86x |
- #' Module to create a `teal` app. This module can be called directly instead of [init()] and+ id, |
||
| 6 | -+ | |||
| 212 | +86x |
- #' included in your custom application. Please note that [init()] adds `reporter_previewer_module`+ list( |
||
| 7 | -+ | |||
| 213 | +86x |
- #' automatically, which is not a case when calling `ui/srv_teal` directly.+ get_available_teal_slices = module_fd()$get_available_teal_slices(), |
||
| 8 | -+ | |||
| 214 | +86x |
- #'+ set_filter_state = module_fd()$set_filter_state, # for testing purpose |
||
| 9 | -+ | |||
| 215 | +86x |
- #' @details+ get_filter_state = module_fd()$get_filter_state # for testing purpose |
||
| 10 | +216 |
- #'+ ) |
||
| 11 | +217 |
- #' Module is responsible for creating the main `shiny` app layout and initializing all the necessary+ ) |
||
| 12 | +218 |
- #' components. This module establishes reactive connection between the input `data` and every other+ }) |
||
| 13 | +219 |
- #' component in the app. Reactive change of the `data` passed as an argument, reloads the app and+ |
||
| 14 | +220 |
- #' possibly keeps all input settings the same so the user can continue where one left off.+ # Update global state and mapping matrix when module filters change. |
||
| 15 | -+ | |||
| 221 | +105x |
- #'+ obs2 <- observeEvent(slices_module(), priority = 0, {
|
||
| 16 | -+ | |||
| 222 | +108x |
- #' ## data flow in `teal` application+ this_slices <- slices_module() |
||
| 17 | -+ | |||
| 223 | +108x |
- #'+ slices_global$slices_append(this_slices) # append new slices to the all_slices list |
||
| 18 | -+ | |||
| 224 | +108x |
- #' This module supports multiple data inputs but eventually, they are all converted to `reactive`+ mapping_elem <- setNames(nm = id, list(vapply(this_slices, `[[`, character(1L), "id"))) |
||
| 19 | -+ | |||
| 225 | +108x |
- #' returning `teal_data` in this module. On this `reactive teal_data` object several actions are+ slices_global$slices_active(mapping_elem) |
||
| 20 | +226 |
- #' performed:+ }) |
||
| 21 | +227 |
- #' - data loading in [`module_init_data`]+ |
||
| 22 | -+ | |||
| 228 | +105x |
- #' - data filtering in [`module_filter_data`]+ obs3 <- observeEvent(slices_global_module(), {
|
||
| 23 | -+ | |||
| 229 | +128x |
- #' - data transformation in [`module_transform_data`]+ global_vs_module <- setdiff_teal_slices(slices_global_module(), slices_module()) |
||
| 24 | -+ | |||
| 230 | +128x |
- #'+ module_vs_global <- setdiff_teal_slices(slices_module(), slices_global_module()) |
||
| 25 | -+ | |||
| 231 | +119x |
- #' ## Fallback on failure+ if (length(global_vs_module) || length(module_vs_global)) {
|
||
| 26 | +232 |
- #'+ # Comment: (Nota Bene) Normally new filters for a module are added through module-filter-panel, and slices |
||
| 27 | +233 |
- #' `teal` is designed in such way that app will never crash if the error is introduced in any+ # global are updated automatically so slices_module -> slices_global_module are equal. |
||
| 28 | +234 |
- #' custom `shiny` module provided by app developer (e.g. [teal_data_module()], [teal_transform_module()]).+ # this if is valid only when a change is made on the global level so the change needs to be propagated down |
||
| 29 | +235 |
- #' If any module returns a failing object, the app will halt the evaluation and display a warning message.+ # to the module (for example through snapshot manager). If it happens both slices are different |
||
| 30 | -+ | |||
| 236 | +13x |
- #' App user should always have a chance to fix the improper input and continue without restarting the session.+ logger::log_debug("srv_module_filter_manager@3 (N.B.) global state has changed for a module:{ id }.")
|
||
| 31 | -+ | |||
| 237 | +13x |
- #'+ module_fd()$clear_filter_states() |
||
| 32 | -+ | |||
| 238 | +13x |
- #' @rdname module_teal+ module_fd()$set_filter_state(slices_global_module()) |
||
| 33 | +239 |
- #' @name module_teal+ } |
||
| 34 | +240 |
- #'+ }) |
||
| 35 | +241 |
- #' @inheritParams module_init_data+ |
||
| 36 | -+ | |||
| 242 | +105x |
- #' @inheritParams init+ slices_module # returned for testing purpose |
||
| 37 | +243 |
- #'+ }) |
||
| 38 | +244 |
- #' @return `NULL` invisibly+ } |
||
| 39 | +245 |
- NULL+ |
||
| 40 | +246 |
-
+ #' @importFrom shiny reactiveVal reactiveValues |
||
| 41 | +247 |
- #' @rdname module_teal+ methods::setOldClass("reactiveVal")
|
||
| 42 | +248 |
- #' @export+ methods::setOldClass("reactivevalues")
|
||
| 43 | +249 |
- ui_teal <- function(id,+ |
||
| 44 | +250 |
- modules,+ #' @importFrom methods new |
||
| 45 | +251 |
- title = build_app_title(),+ #' @rdname module_filter_manager |
||
| 46 | +252 |
- header = tags$p(),+ .slicesGlobal <- methods::setRefClass(".slicesGlobal", # nolint: object_name.
|
||
| 47 | +253 |
- footer = tags$p()) {
- |
- ||
| 48 | -! | -
- checkmate::assert_character(id, max.len = 1, any.missing = FALSE)- |
- ||
| 49 | -! | -
- checkmate::assert(- |
- ||
| 50 | -! | -
- .var.name = "title",+ fields = list( |
||
| 51 | -! | +|||
| 254 | +
- checkmate::check_string(title),+ all_slices = "reactiveVal", |
|||
| 52 | -! | +|||
| 255 | +
- checkmate::check_multi_class(title, c("shiny.tag", "shiny.tag.list", "html"))
+ module_slices_api = "reactivevalues" |
|||
| 53 | +256 |
- )+ ), |
||
| 54 | -! | +|||
| 257 | +
- checkmate::assert(+ methods = list( |
|||
| 55 | -! | +|||
| 258 | +
- .var.name = "header",+ initialize = function(slices = teal_slices(), module_labels) {
|
|||
| 56 | -! | +|||
| 259 | +80x |
- checkmate::check_string(header),+ shiny::isolate({
|
||
| 57 | -! | +|||
| 260 | +80x |
- checkmate::check_multi_class(header, c("shiny.tag", "shiny.tag.list", "html"))
+ checkmate::assert_class(slices, "teal_slices") |
||
| 58 | +261 |
- )- |
- ||
| 59 | -! | -
- checkmate::assert(+ # needed on init to not mix "global_filters" with module-specific-slots |
||
| 60 | -! | +|||
| 262 | +80x |
- .var.name = "footer",+ if (isTRUE(attr(slices, "module_specific"))) {
|
||
| 61 | -! | +|||
| 263 | +11x |
- checkmate::check_string(footer),+ old_mapping <- attr(slices, "mapping") |
||
| 62 | -! | +|||
| 264 | +11x |
- checkmate::check_multi_class(footer, c("shiny.tag", "shiny.tag.list", "html"))
+ new_mapping <- sapply(module_labels, simplify = FALSE, function(module_label) {
|
||
| 63 | -+ | |||
| 265 | +20x |
- )+ unique(unlist(old_mapping[c(module_label, "global_filters")])) |
||
| 64 | +266 | - - | -||
| 65 | -! | -
- if (is.character(title)) {
+ }) |
||
| 66 | -! | +|||
| 267 | +11x |
- title <- build_app_title(title)+ attr(slices, "mapping") <- new_mapping |
||
| 67 | +268 |
- } else {
- |
- ||
| 68 | -! | -
- validate_app_title_tag(title)+ } |
||
| 69 | -+ | |||
| 269 | +80x |
- }+ .self$all_slices <<- shiny::reactiveVal(slices) |
||
| 70 | -+ | |||
| 270 | +80x |
-
+ .self$module_slices_api <<- shiny::reactiveValues() |
||
| 71 | -! | +|||
| 271 | +80x |
- if (checkmate::test_string(header)) {
+ .self$slices_append(slices) |
||
| 72 | -! | +|||
| 272 | +80x |
- header <- tags$p(header)+ .self$slices_active(attr(slices, "mapping")) |
||
| 73 | -+ | |||
| 273 | +80x |
- }+ invisible(.self) |
||
| 74 | +274 | - - | -||
| 75 | -! | -
- if (checkmate::test_string(footer)) {
- |
- ||
| 76 | -! | -
- footer <- tags$p(footer)+ }) |
||
| 77 | +275 |
- }+ }, |
||
| 78 | +276 |
-
+ is_module_specific = function() {
|
||
| 79 | -! | +|||
| 277 | +277x |
- ns <- NS(id)+ isTRUE(attr(.self$all_slices(), "module_specific")) |
||
| 80 | +278 |
-
+ }, |
||
| 81 | +279 |
- # show busy icon when `shiny` session is busy computing stuff+ module_slices_api_set = function(module_label, functions_list) {
|
||
| 82 | -+ | |||
| 280 | +86x |
- # based on https://stackoverflow.com/questions/17325521/r-shiny-display-loading-message-while-function-is-running/22475216#22475216 # nolint: line_length.+ shiny::isolate({
|
||
| 83 | -! | +|||
| 281 | +86x |
- shiny_busy_message_panel <- conditionalPanel(+ if (!.self$is_module_specific()) {
|
||
| 84 | -! | +|||
| 282 | +70x |
- condition = "(($('html').hasClass('shiny-busy')) && (document.getElementById('shiny-notification-panel') == null))", # nolint: line_length.
+ module_label <- "global_filters" |
||
| 85 | -! | +|||
| 283 | +
- tags$div(+ } |
|||
| 86 | -! | +|||
| 284 | +86x |
- icon("arrows-rotate", class = "fa-spin", prefer_type = "solid"),
+ if (!identical(.self$module_slices_api[[module_label]], functions_list)) {
|
||
| 87 | -! | +|||
| 285 | +86x |
- "Computing ...",+ .self$module_slices_api[[module_label]] <- functions_list |
||
| 88 | +286 |
- # CSS defined in `custom.css`+ } |
||
| 89 | -! | +|||
| 287 | +86x |
- class = "shinybusymessage"+ invisible(.self) |
||
| 90 | +288 |
- )+ }) |
||
| 91 | +289 |
- )+ }, |
||
| 92 | +290 |
-
+ slices_deactivate_all = function(module_label) {
|
||
| 93 | +291 | ! |
- fluidPage(+ shiny::isolate({
|
|
| 94 | +292 | ! |
- id = id,+ new_slices <- .self$all_slices() |
|
| 95 | +293 | ! |
- title = title,+ old_mapping <- attr(new_slices, "mapping") |
|
| 96 | -! | +|||
| 294 | +
- theme = get_teal_bs_theme(),+ |
|||
| 97 | +295 | ! |
- include_teal_css_js(),+ new_mapping <- if (.self$is_module_specific()) {
|
|
| 98 | +296 | ! |
- tags$header(header),+ new_module_mapping <- setNames(nm = module_label, list(character(0))) |
|
| 99 | +297 | ! |
- tags$hr(class = "my-2"),+ modifyList(old_mapping, new_module_mapping) |
|
| 100 | +298 | ! |
- shiny_busy_message_panel,+ } else if (missing(module_label)) {
|
|
| 101 | +299 | ! |
- tags$div(+ lapply( |
|
| 102 | +300 | ! |
- id = ns("tabpanel_wrapper"),
+ attr(.self$all_slices(), "mapping"), |
|
| 103 | +301 | ! |
- class = "teal-body",+ function(x) character(0) |
|
| 104 | -! | +|||
| 302 | +
- ui_teal_module(id = ns("teal_modules"), modules = modules)
+ ) |
|||
| 105 | +303 |
- ),+ } else {
|
||
| 106 | +304 | ! |
- tags$div(+ old_mapping[[module_label]] <- character(0) |
|
| 107 | +305 | ! |
- id = ns("options_buttons"),
+ old_mapping |
|
| 108 | -! | +|||
| 306 | +
- style = "position: absolute; right: 10px;",+ } |
|||
| 109 | -! | +|||
| 307 | +
- ui_bookmark_panel(ns("bookmark_manager"), modules),
+
|
|||
| 110 | +308 | ! |
- tags$button(+ if (!identical(new_mapping, old_mapping)) {
|
|
| 111 | +309 | ! |
- class = "btn action-button filter_hamburger", # see sidebar.css for style filter_hamburger+ logger::log_debug(".slicesGlobal@slices_deactivate_all: deactivating all slices.")
|
|
| 112 | +310 | ! |
- href = "javascript:void(0)",+ attr(new_slices, "mapping") <- new_mapping |
|
| 113 | +311 | ! |
- onclick = sprintf("toggleFilterPanel('%s');", ns("tabpanel_wrapper")),
+ .self$all_slices(new_slices) |
|
| 114 | -! | +|||
| 312 | +
- title = "Toggle filter panel",+ } |
|||
| 115 | +313 | ! |
- icon("fas fa-bars")
+ invisible(.self) |
|
| 116 | +314 |
- ),- |
- ||
| 117 | -! | -
- ui_snapshot_manager_panel(ns("snapshot_manager_panel")),
+ }) |
||
| 118 | -! | +|||
| 315 | +
- ui_filter_manager_panel(ns("filter_manager_panel"))
+ }, |
|||
| 119 | +316 |
- ),+ slices_active = function(mapping_elem) {
|
||
| 120 | -! | +|||
| 317 | +191x |
- tags$script(+ shiny::isolate({
|
||
| 121 | -! | -
- HTML(- |
- ||
| 122 | -! | -
- sprintf(- |
- ||
| 123 | -- |
- "- |
- ||
| 124 | -! | -
- $(document).ready(function() {
- |
- ||
| 125 | -! | +|||
| 318 | +191x |
- $('#%s').appendTo('#%s');
+ if (.self$is_module_specific()) {
|
||
| 126 | -+ | |||
| 319 | +36x |
- });+ new_mapping <- modifyList(attr(.self$all_slices(), "mapping"), mapping_elem) |
||
| 127 | +320 |
- ",- |
- ||
| 128 | -! | -
- ns("options_buttons"),
- |
- ||
| 129 | -! | -
- ns("teal_modules-active_tab")
+ } else {
|
||
| 130 | -+ | |||
| 321 | +155x |
- )+ new_mapping <- setNames(nm = "global_filters", list(unique(unlist(mapping_elem)))) |
||
| 131 | +322 |
- )+ } |
||
| 132 | +323 |
- ),- |
- ||
| 133 | -! | -
- tags$hr(),- |
- ||
| 134 | -! | -
- tags$footer(+ |
||
| 135 | -! | +|||
| 324 | +191x |
- tags$div(+ if (!identical(new_mapping, attr(.self$all_slices(), "mapping"))) {
|
||
| 136 | -! | +|||
| 325 | +134x |
- footer,+ mapping_modules <- toString(names(new_mapping)) |
||
| 137 | -! | +|||
| 326 | +134x |
- teal.widgets::verbatim_popup_ui(ns("sessionInfo"), "Session Info", type = "link"),
+ logger::log_debug(".slicesGlobal@slices_active: changing mapping for module(s): { mapping_modules }.")
|
||
| 138 | -! | +|||
| 327 | +134x |
- br(),+ new_slices <- .self$all_slices() |
||
| 139 | -! | +|||
| 328 | +134x |
- ui_teal_lockfile(ns("lockfile")),
+ attr(new_slices, "mapping") <- new_mapping |
||
| 140 | -! | +|||
| 329 | +134x |
- textOutput(ns("identifier"))
+ .self$all_slices(new_slices) |
||
| 141 | +330 |
- )+ } |
||
| 142 | +331 |
- )+ |
||
| 143 | -+ | |||
| 332 | +191x |
- )+ invisible(.self) |
||
| 144 | +333 |
- }+ }) |
||
| 145 | +334 |
-
+ }, |
||
| 146 | +335 |
- #' @rdname module_teal+ # - only new filters are appended to the $all_slices |
||
| 147 | +336 |
- #' @export+ # - mapping is not updated here |
||
| 148 | +337 |
- srv_teal <- function(id, data, modules, filter = teal_slices()) {
+ slices_append = function(slices, activate = FALSE) {
|
||
| 149 | -79x - | +338 | +191x |
- checkmate::assert_character(id, max.len = 1, any.missing = FALSE)+ shiny::isolate({
|
| 150 | -79x - | +339 | +191x |
- checkmate::assert_multi_class(data, c("teal_data", "teal_data_module", "reactive"))
+ if (!is.teal_slices(slices)) {
|
| 151 | -78x - | +|||
| 340 | +! |
- checkmate::assert_class(modules, "teal_modules")+ slices <- as.teal_slices(slices) |
||
| 152 | -78x - | +|||
| 341 | +
- checkmate::assert_class(filter, "teal_slices")+ } |
|||
| 153 | +342 | |||
| 154 | -78x - | +|||
| 343 | +
- moduleServer(id, function(input, output, session) {
+ # to make sure that we don't unnecessary trigger $all_slices <reactiveVal> |
|||
| 155 | -78x - | +344 | +191x |
- logger::log_debug("srv_teal initializing.")
+ new_slices <- setdiff_teal_slices(slices, .self$all_slices()) |
| 156 | -+ | |||
| 345 | +191x |
-
+ old_mapping <- attr(.self$all_slices(), "mapping") |
||
| 157 | -78x - | +346 | +191x |
- if (getOption("teal.show_js_log", default = FALSE)) {
+ if (length(new_slices)) {
|
| 158 | -! | +|||
| 347 | +6x |
- shinyjs::showLog()+ new_ids <- vapply(new_slices, `[[`, character(1L), "id") |
||
| 159 | -+ | |||
| 348 | +6x |
- }+ logger::log_debug(".slicesGlobal@slices_append: appending new slice(s): { new_ids }.")
|
||
| 160 | -+ | |||
| 349 | +6x |
-
+ slices_ids <- vapply(.self$all_slices(), `[[`, character(1L), "id") |
||
| 161 | -78x - | +350 | +6x |
- srv_teal_lockfile("lockfile")
+ lapply(new_slices, function(slice) {
|
| 162 | +351 |
-
+ # In case the new state has the same id as an existing one, add a suffix |
||
| 163 | -78x - | +352 | +6x |
- output$identifier <- renderText(+ if (slice$id %in% slices_ids) {
|
| 164 | -78x - | +353 | +1x |
- paste0("Pid:", Sys.getpid(), " Token:", substr(session$token, 25, 32))
+ slice$id <- utils::tail(make.unique(c(slices_ids, slice$id), sep = "_"), 1) |
| 165 | +354 |
- )+ } |
||
| 166 | +355 |
-
+ }) |
||
| 167 | -78x - | +|||
| 356 | +
- teal.widgets::verbatim_popup_srv(+ |
|||
| 168 | -78x - | +357 | +6x |
- "sessionInfo",+ new_slices_all <- c(.self$all_slices(), new_slices) |
| 169 | -78x - | +358 | +6x |
- verbatim_content = utils::capture.output(utils::sessionInfo()),+ attr(new_slices_all, "mapping") <- old_mapping |
| 170 | -78x - | +359 | +6x |
- title = "SessionInfo"+ .self$all_slices(new_slices_all) |
| 171 | +360 |
- )+ } |
||
| 172 | +361 | |||
| 173 | -- |
- # `JavaScript` code- |
- ||
| 174 | -78x - | +362 | +191x |
- run_js_files(files = "init.js")+ invisible(.self) |
| 175 | +363 |
-
+ }) |
||
| 176 | +364 |
- # set timezone in shiny app+ }, |
||
| 177 | +365 |
- # timezone is set in the early beginning so it will be available also+ slices_get = function(module_label) {
|
||
| 178 | -+ | |||
| 366 | +283x |
- # for `DDL` and all shiny modules+ if (missing(module_label)) {
|
||
| 179 | -78x - | +|||
| 367 | +! |
- get_client_timezone(session$ns)+ .self$all_slices() |
||
| 180 | -78x - | +|||
| 368 | +
- observeEvent(+ } else {
|
|||
| 181 | -78x - | +369 | +283x |
- eventExpr = input$timezone,+ module_ids <- unlist(attr(.self$all_slices(), "mapping")[c(module_label, "global_filters")]) |
| 182 | -78x - | +370 | +283x |
- once = TRUE,+ Filter( |
| 183 | -78x - | +371 | +283x |
- handlerExpr = {
+ function(slice) slice$id %in% module_ids, |
| 184 | -! | +|||
| 372 | +283x |
- session$userData$timezone <- input$timezone+ .self$all_slices() |
||
| 185 | -! | +|||
| 373 | +
- logger::log_debug("srv_teal@1 Timezone set to client's timezone: { input$timezone }.")
+ ) |
|||
| 186 | +374 |
} |
||
| 187 | +375 |
- )+ }, |
||
| 188 | +376 |
-
+ slices_set = function(slices) {
|
||
| 189 | -78x - | +377 | +7x |
- data_pulled <- srv_init_data("data", data = data)
+ shiny::isolate({
|
| 190 | -77x - | +378 | +7x |
- data_validated <- srv_validate_reactive_teal_data(+ if (!is.teal_slices(slices)) {
|
| 191 | -77x - | +|||
| 379 | +! |
- "validate",+ slices <- as.teal_slices(slices) |
||
| 192 | -77x - | +|||
| 380 | +
- data = data_pulled,+ } |
|||
| 193 | -77x - | +381 | +7x |
- modules = modules,+ .self$all_slices(slices) |
| 194 | -77x - | +382 | +7x |
- validate_shiny_silent_error = FALSE+ invisible(.self) |
| 195 | +383 |
- )+ }) |
||
| 196 | -77x - | +|||
| 384 | +
- data_rv <- reactive({
+ }, |
|||
| 197 | -132x - | +|||
| 385 | +
- req(inherits(data_validated(), "teal_data"))+ show = function() {
|
|||
| 198 | -65x - | +|||
| 386 | +! |
- is_filter_ok <- check_filter_datanames(filter, ls(teal.code::get_env(data_validated())))+ shiny::isolate(print(.self$all_slices())) |
||
| 199 | -65x - | +|||
| 387 | +! |
- if (!isTRUE(is_filter_ok)) {
+ invisible(.self) |
||
| 200 | -2x - | +|||
| 388 | +
- showNotification(+ } |
|||
| 201 | -2x - | +|||
| 389 | +
- "Some filters were not applied because of incompatibility with data. Contact app developer.",+ ) |
|||
| 202 | -2x - | +|||
| 390 | +
- type = "warning",+ ) |
|||
| 203 | -2x - | +|||
| 391 | +
- duration = 10+ # todo: prevent any teal_slices attribute except mapping |
| 204 | +1 |
- )+ #' Calls all `modules` |
|
| 205 | -2x - | +||
| 2 | +
- warning(is_filter_ok)+ #' |
||
| 206 | +3 |
- }+ #' On the UI side each `teal_modules` is translated to a `tabsetPanel` and each `teal_module` is a |
|
| 207 | -65x - | +||
| 4 | +
- .add_signature_to_data(data_validated())+ #' `tabPanel`. Both, UI and server are called recursively so that each tab is a separate module and |
||
| 208 | +5 |
- })+ #' reflect nested structure of `modules` argument. |
|
| 209 | +6 |
-
+ #' |
|
| 210 | -77x - | +||
| 7 | +
- data_load_status <- reactive({
+ #' @name module_teal_module |
||
| 211 | -70x - | +||
| 8 | +
- if (inherits(data_pulled(), "teal_data")) {
+ #' |
||
| 212 | -65x - | +||
| 9 | +
- "ok"+ #' @inheritParams module_teal |
||
| 213 | -5x - | -
- } else if (inherits(data, "teal_data_module")) {
- |
- |
| 214 | -5x - | +||
| 10 | +
- "teal_data_module failed"+ #' |
||
| 215 | +11 |
- } else {
+ #' @param data_rv (`reactive` returning `teal_data`) |
|
| 216 | -! | +||
| 12 | +
- "external failed"+ #' |
||
| 217 | +13 |
- }+ #' @param slices_global (`reactiveVal` returning `modules_teal_slices`) |
|
| 218 | +14 |
- })+ #' see [`module_filter_manager`] |
|
| 219 | +15 |
-
+ #' |
|
| 220 | -77x - | +||
| 16 | +
- datasets_rv <- if (!isTRUE(attr(filter, "module_specific"))) {
+ #' @param depth (`integer(1)`) |
||
| 221 | -66x - | +||
| 17 | +
- eventReactive(data_rv(), {
+ #' number which helps to determine depth of the modules nesting. |
||
| 222 | -56x - | +||
| 18 | +
- req(inherits(data_rv(), "teal_data"))+ #' |
||
| 223 | -56x - | +||
| 19 | +
- logger::log_debug("srv_teal@1 initializing FilteredData")
+ #' @param datasets (`reactive` returning `FilteredData` or `NULL`) |
||
| 224 | -56x - | +||
| 20 | +
- teal_data_to_filtered_data(data_rv())+ #' When `datasets` is passed from the parent module (`srv_teal`) then `dataset` is a singleton |
||
| 225 | +21 |
- })+ #' which implies in filter-panel to be "global". When `NULL` then filter-panel is "module-specific". |
|
| 226 | +22 |
- }+ #' |
|
| 227 | +23 |
-
+ #' @param data_load_status (`reactive` returning `character`) |
|
| 228 | -77x - | +||
| 24 | +
- if (inherits(data, "teal_data_module")) {
+ #' Determines action dependent on a data loading status: |
||
| 229 | -9x - | +||
| 25 | +
- setBookmarkExclude(c("teal_modules-active_tab"))
+ #' - `"ok"` when `teal_data` is returned from the data loading. |
||
| 230 | -9x - | +||
| 26 | +
- shiny::insertTab(+ #' - `"teal_data_module failed"` when [teal_data_module()] didn't return `teal_data`. Disables tabs buttons. |
||
| 231 | -9x - | +||
| 27 | +
- inputId = "teal_modules-active_tab",+ #' - `"external failed"` when a `reactive` passed to `srv_teal(data)` didn't return `teal_data`. Hides the whole tab |
||
| 232 | -9x - | +||
| 28 | +
- position = "before",+ #' panel. |
||
| 233 | -9x - | +||
| 29 | +
- select = TRUE,+ #' |
||
| 234 | -9x - | +||
| 30 | +
- tabPanel(+ #' @return |
||
| 235 | -9x - | +||
| 31 | +
- title = icon("fas fa-database"),
+ #' output of currently active module. |
||
| 236 | -9x - | +||
| 32 | +
- value = "teal_data_module",+ #' - `srv_teal_module.teal_module` returns `reactiveVal` containing output of the called module. |
||
| 237 | -9x - | +||
| 33 | +
- tags$div(+ #' - `srv_teal_module.teal_modules` returns output of module selected by `input$active_tab`. |
||
| 238 | -9x - | +||
| 34 | +
- ui_init_data(session$ns("data")),
+ #' |
||
| 239 | -9x - | +||
| 35 | +
- ui_validate_reactive_teal_data(session$ns("validate"))
+ #' @keywords internal |
||
| 240 | +36 |
- )+ NULL |
|
| 241 | +37 |
- )+ |
|
| 242 | +38 |
- )+ #' @rdname module_teal_module |
|
| 243 | +39 |
-
+ ui_teal_module <- function(id, modules, depth = 0L) {
|
|
| 244 | -9x - | +||
| 40 | +! |
- if (attr(data, "once")) {
+ checkmate::assert_multi_class(modules, c("teal_modules", "teal_module", "shiny.tag"))
|
|
| 245 | -9x - | +||
| 41 | +! |
- observeEvent(data_rv(), once = TRUE, {
+ checkmate::assert_count(depth) |
|
| 246 | -4x - | +||
| 42 | +! |
- logger::log_debug("srv_teal@2 removing data tab.")
+ UseMethod("ui_teal_module", modules)
|
|
| 247 | +43 |
- # when once = TRUE we pull data once and then remove data tab- |
- |
| 248 | -4x - | -
- removeTab("teal_modules-active_tab", target = "teal_data_module")
+ } |
|
| 249 | +44 |
- })+ |
|
| 250 | +45 |
- }+ #' @rdname module_teal_module |
|
| 251 | +46 |
- } else {
+ #' @export |
|
| 252 | +47 |
- # when no teal_data_module then we want to display messages above tabsetPanel (because there is no data-tab)+ ui_teal_module.default <- function(id, modules, depth = 0L) {
|
|
| 253 | -68x - | +||
| 48 | +! |
- insertUI(+ stop("Modules class not supported: ", paste(class(modules), collapse = " "))
|
|
| 254 | -68x - | +||
| 49 | +
- selector = sprintf("#%s", session$ns("tabpanel_wrapper")),
+ } |
||
| 255 | -68x - | +||
| 50 | +
- where = "beforeBegin",+ |
||
| 256 | -68x - | +||
| 51 | +
- ui = tags$div(ui_validate_reactive_teal_data(session$ns("validate")), tags$br())
+ #' @rdname module_teal_module |
||
| 257 | +52 |
- )+ #' @export |
|
| 258 | +53 |
- }+ ui_teal_module.teal_modules <- function(id, modules, depth = 0L) {
|
|
| 259 | -+ | ||
| 54 | +! |
-
+ ns <- NS(id) |
|
| 260 | -77x - | +||
| 55 | +! |
- module_labels <- unlist(module_labels(modules), use.names = FALSE)+ tags$div( |
|
| 261 | -77x - | +||
| 56 | +! |
- slices_global <- methods::new(".slicesGlobal", filter, module_labels)
+ id = ns("wrapper"),
|
|
| 262 | -77x - | +||
| 57 | +! |
- modules_output <- srv_teal_module(+ do.call( |
|
| 263 | -77x - | +||
| 58 | +! |
- id = "teal_modules",+ tabsetPanel, |
|
| 264 | -77x - | +||
| 59 | +! |
- data_rv = data_rv,+ c( |
|
| 265 | -77x - | +||
| 60 | +
- datasets = datasets_rv,+ # by giving an id, we can reactively respond to tab changes |
||
| 266 | -77x - | +||
| 61 | +! |
- modules = modules,+ list( |
|
| 267 | -77x - | +||
| 62 | +! |
- slices_global = slices_global,+ id = ns("active_tab"),
|
|
| 268 | -77x - | +||
| 63 | +! |
- data_load_status = data_load_status+ type = if (modules$label == "root") "pills" else "tabs" |
|
| 269 | +64 |
- )+ ), |
|
| 270 | -77x - | +||
| 65 | +! |
- mapping_table <- srv_filter_manager_panel("filter_manager_panel", slices_global = slices_global)
+ lapply( |
|
| 271 | -77x - | +||
| 66 | +! |
- snapshots <- srv_snapshot_manager_panel("snapshot_manager_panel", slices_global = slices_global)
+ names(modules$children), |
|
| 272 | -77x - | +||
| 67 | +! |
- srv_bookmark_panel("bookmark_manager", modules)
+ function(module_id) {
|
|
| 273 | -+ | ||
| 68 | +! |
- })+ module_label <- modules$children[[module_id]]$label |
|
| 274 | -+ | ||
| 69 | +! |
-
+ if (is.null(module_label)) {
|
|
| 275 | -77x - | +||
| 70 | +! |
- invisible(NULL)+ module_label <- icon("fas fa-database")
|
|
| 276 | +71 |
- }+ } |
| 1 | -+ | |||
| 72 | +! |
- #' Filter state snapshot management+ tabPanel( |
||
| 2 | -+ | |||
| 73 | +! |
- #'+ title = module_label, |
||
| 3 | -+ | |||
| 74 | +! |
- #' Capture and restore snapshots of the global (app) filter state.+ value = module_id, # when clicked this tab value changes input$<tabset panel id> |
||
| 4 | -+ | |||
| 75 | +! |
- #'+ ui_teal_module( |
||
| 5 | -+ | |||
| 76 | +! |
- #' This module introduces snapshots: stored descriptions of the filter state of the entire application.+ id = ns(module_id), |
||
| 6 | -+ | |||
| 77 | +! |
- #' Snapshots allow the user to save the current filter state of the application for later use in the session,+ modules = modules$children[[module_id]], |
||
| 7 | -+ | |||
| 78 | +! |
- #' as well as to save it to file in order to share it with an app developer or other users,+ depth = depth + 1L |
||
| 8 | +79 |
- #' who in turn can upload it to their own session.+ ) |
||
| 9 | +80 |
- #'+ ) |
||
| 10 | +81 |
- #' The snapshot manager is accessed with the camera icon in the tabset bar.+ } |
||
| 11 | +82 |
- #' At the beginning of a session it presents three icons: a camera, an upload, and an circular arrow.+ ) |
||
| 12 | +83 |
- #' Clicking the camera captures a snapshot, clicking the upload adds a snapshot from a file+ ) |
||
| 13 | +84 |
- #' and applies the filter states therein, and clicking the arrow resets initial application state.+ ) |
||
| 14 | +85 |
- #' 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 | +86 |
- #'+ } |
||
| 16 | +87 |
- #' @section Server logic:+ |
||
| 17 | +88 |
- #' Snapshots are basically `teal_slices` objects, however, since each module is served by a separate instance+ #' @rdname module_teal_module |
||
| 18 | +89 |
- #' of `FilteredData` and these objects require shared state, `teal_slice` is a `reactiveVal` so `teal_slices`+ #' @export |
||
| 19 | +90 |
- #' cannot be stored as is. Therefore, `teal_slices` are reversibly converted to a list of lists representation+ ui_teal_module.teal_module <- function(id, modules, depth = 0L) {
|
||
| 20 | -+ | |||
| 91 | +! |
- #' (attributes are maintained).+ ns <- NS(id) |
||
| 21 | -+ | |||
| 92 | +! |
- #'+ args <- c(list(id = ns("module")), modules$ui_args)
|
||
| 22 | +93 |
- #' Snapshots are stored in a `reactiveVal` as a named list.+ |
||
| 23 | -+ | |||
| 94 | +! |
- #' The first snapshot is the initial state of the application and the user can add a snapshot whenever they see fit.+ ui_teal <- tagList( |
||
| 24 | -+ | |||
| 95 | +! |
- #'+ div( |
||
| 25 | -+ | |||
| 96 | +! |
- #' For every snapshot except the initial one, a piece of UI is generated that contains+ id = ns("validate_datanames"),
|
||
| 26 | -+ | |||
| 97 | +! |
- #' the snapshot name, a select button to restore that snapshot, and a save button to save it to a file.+ ui_validate_reactive_teal_data(ns("validate_datanames"))
|
||
| 27 | +98 |
- #' The initial snapshot is restored by a separate "reset" button.+ ), |
||
| 28 | -+ | |||
| 99 | +! |
- #' It cannot be saved directly but a user is welcome to capture the initial state as a snapshot and save that.+ shinyjs::hidden( |
||
| 29 | -+ | |||
| 100 | +! |
- #'+ tags$div( |
||
| 30 | -+ | |||
| 101 | +! |
- #' @section Snapshot mechanics:+ id = ns("transformer_failure_info"),
|
||
| 31 | -+ | |||
| 102 | +! |
- #' When a snapshot is captured, the user is prompted to name it.+ class = "teal_validated", |
||
| 32 | -+ | |||
| 103 | +! |
- #' Names are displayed as is but since they are used to create button ids,+ div( |
||
| 33 | -+ | |||
| 104 | +! |
- #' under the hood they are converted to syntactically valid strings.+ class = "teal-output-warning", |
||
| 34 | -+ | |||
| 105 | +! |
- #' New snapshot names are validated so that their valid versions are unique.+ "One of transformers failed. Please fix and continue." |
||
| 35 | +106 |
- #' Leading and trailing white space is trimmed.+ ) |
||
| 36 | +107 |
- #'+ ) |
||
| 37 | +108 |
- #' The module can read the global state of the application from `slices_global` and `mapping_matrix`.+ ), |
||
| 38 | -+ | |||
| 109 | +! |
- #' The former provides a list of all existing `teal_slice`s and the latter says which slice is active in which module.+ tags$div( |
||
| 39 | -+ | |||
| 110 | +! |
- #' Once a name has been accepted, `slices_global` is converted to a list of lists - a snapshot.+ id = ns("teal_module_ui"),
|
||
| 40 | -+ | |||
| 111 | +! |
- #' The snapshot contains the `mapping` attribute of the initial application state+ do.call(modules$ui, args) |
||
| 41 | +112 |
- #' (or one that has been restored), which may not reflect the current one,+ ) |
||
| 42 | +113 |
- #' so `mapping_matrix` is transformed to obtain the current mapping, i.e. a list that,+ ) |
||
| 43 | +114 |
- #' when passed to the `mapping` argument of [teal_slices()], would result in the current mapping.+ |
||
| 44 | -+ | |||
| 115 | +! |
- #' This is substituted as the snapshot's `mapping` attribute and the snapshot is added to the snapshot list.+ div( |
||
| 45 | -+ | |||
| 116 | +! |
- #'+ id = id, |
||
| 46 | -+ | |||
| 117 | +! |
- #' To restore app state, a snapshot is retrieved from storage and rebuilt into a `teal_slices` object.+ class = "teal_module", |
||
| 47 | -+ | |||
| 118 | +! |
- #' Then state of all `FilteredData` objects (provided in `datasets`) is cleared+ uiOutput(ns("data_reactive"), inline = TRUE),
|
||
| 48 | -+ | |||
| 119 | +! |
- #' and set anew according to the `mapping` attribute of the snapshot.+ tagList( |
||
| 49 | -+ | |||
| 120 | +! |
- #' The snapshot is then set as the current content of `slices_global`.+ if (depth >= 2L) tags$div(style = "mt-6"), |
||
| 50 | -+ | |||
| 121 | +! |
- #'+ if (!is.null(modules$datanames)) {
|
||
| 51 | -+ | |||
| 122 | +! |
- #' To save a snapshot, the snapshot is retrieved and reassembled just like for restoring,+ fluidRow( |
||
| 52 | -+ | |||
| 123 | +! |
- #' and then saved to file with [slices_store()].+ column(width = 9, ui_teal, class = "teal_primary_col"), |
||
| 53 | -+ | |||
| 124 | +! |
- #'+ column( |
||
| 54 | -+ | |||
| 125 | +! |
- #' When a snapshot is uploaded, it will first be added to storage just like a newly created one,+ width = 3, |
||
| 55 | -+ | |||
| 126 | +! |
- #' and then used to restore app state much like a snapshot taken from storage.+ ui_data_summary(ns("data_summary")),
|
||
| 56 | -+ | |||
| 127 | +! |
- #' Upon clicking the upload icon the user will be prompted for a file to upload+ ui_filter_data(ns("filter_panel")),
|
||
| 57 | -+ | |||
| 128 | +! |
- #' and may choose to name the new snapshot. The name defaults to the name of the file (the extension is dropped)+ ui_transform_data(ns("data_transform"), transformers = modules$transformers, class = "well"),
|
||
| 58 | -+ | |||
| 129 | +! |
- #' and normal naming rules apply. Loading the file yields a `teal_slices` object,+ class = "teal_secondary_col" |
||
| 59 | +130 |
- #' which is disassembled for storage and used directly for restoring app state.+ ) |
||
| 60 | +131 |
- #'+ ) |
||
| 61 | +132 |
- #' @section Transferring snapshots:+ } else {
|
||
| 62 | -+ | |||
| 133 | +! |
- #' Snapshots uploaded from disk should only be used in the same application they come from,+ div( |
||
| 63 | -+ | |||
| 134 | +! |
- #' _i.e._ an application that uses the same data and the same modules.+ div( |
||
| 64 | -+ | |||
| 135 | +! |
- #' To ensure this is the case, `init` stamps `teal_slices` with an app id that is stored in the `app_id` attribute of+ class = "teal_validated", |
||
| 65 | -+ | |||
| 136 | +! |
- #' a `teal_slices` object. When a snapshot is restored from file, its `app_id` is compared to that+ uiOutput(ns("data_input_error"))
|
||
| 66 | +137 |
- #' of the current app state and only if the match is the snapshot admitted to the session.+ ), |
||
| 67 | -+ | |||
| 138 | +! |
- #'+ ui_teal |
||
| 68 | +139 |
- #' @section Bookmarks:+ ) |
||
| 69 | +140 |
- #' An `onBookmark` callback creates a snapshot of the current filter state.+ } |
||
| 70 | +141 |
- #' This is done on the app session, not the module session.+ ) |
||
| 71 | +142 |
- #' (The snapshot will be retrieved by `module_teal` in order to set initial app state in a restored app.)+ ) |
||
| 72 | +143 |
- #' Then that snapshot, and the previous snapshot history are dumped into the `values.rds` file in `<bookmark_dir>`.+ } |
||
| 73 | +144 |
- #'+ |
||
| 74 | +145 |
- #' @param id (`character(1)`) `shiny` module instance id.+ #' @rdname module_teal_module |
||
| 75 | +146 |
- #' @param slices_global (`reactiveVal`) that contains a `teal_slices` object+ srv_teal_module <- function(id, |
||
| 76 | +147 |
- #' containing all `teal_slice`s existing in the app, both active and inactive.+ data_rv, |
||
| 77 | +148 |
- #'+ modules, |
||
| 78 | +149 |
- #' @return `list` containing the snapshot history, where each element is an unlisted `teal_slices` object.+ datasets = NULL, |
||
| 79 | +150 |
- #'+ slices_global, |
||
| 80 | +151 |
- #' @name module_snapshot_manager+ reporter = teal.reporter::Reporter$new(), |
||
| 81 | +152 |
- #' @rdname module_snapshot_manager+ data_load_status = reactive("ok"),
|
||
| 82 | +153 |
- #'+ is_active = reactive(TRUE)) {
|
||
| 83 | -+ | |||
| 154 | +185x |
- #' @author Aleksander Chlebowski+ checkmate::assert_string(id) |
||
| 84 | -+ | |||
| 155 | +185x |
- #' @keywords internal+ assert_reactive(data_rv) |
||
| 85 | -+ | |||
| 156 | +185x |
- NULL+ checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"))
|
||
| 86 | -+ | |||
| 157 | +185x |
-
+ assert_reactive(datasets, null.ok = TRUE) |
||
| 87 | -+ | |||
| 158 | +185x |
- #' @rdname module_snapshot_manager+ checkmate::assert_class(slices_global, ".slicesGlobal") |
||
| 88 | -+ | |||
| 159 | +185x |
- ui_snapshot_manager_panel <- function(id) {
+ checkmate::assert_class(reporter, "Reporter") |
||
| 89 | -! | +|||
| 160 | +185x |
- ns <- NS(id)+ assert_reactive(data_load_status) |
||
| 90 | -! | +|||
| 161 | +185x |
- tags$button(+ UseMethod("srv_teal_module", modules)
|
||
| 91 | -! | +|||
| 162 | +
- id = ns("show_snapshot_manager"),
+ } |
|||
| 92 | -! | +|||
| 163 | +
- class = "btn action-button wunder_bar_button",+ |
|||
| 93 | -! | +|||
| 164 | +
- title = "View filter mapping",+ #' @rdname module_teal_module |
|||
| 94 | -! | +|||
| 165 | +
- suppressMessages(icon("fas fa-camera"))
+ #' @export |
|||
| 95 | +166 |
- )+ srv_teal_module.default <- function(id, |
||
| 96 | +167 |
- }+ data_rv, |
||
| 97 | +168 |
-
+ modules, |
||
| 98 | +169 |
- #' @rdname module_snapshot_manager+ datasets = NULL, |
||
| 99 | +170 |
- srv_snapshot_manager_panel <- function(id, slices_global) {
+ slices_global, |
||
| 100 | -77x - | +|||
| 171 | +
- moduleServer(id, function(input, output, session) {
+ reporter = teal.reporter::Reporter$new(), |
|||
| 101 | -77x - | +|||
| 172 | +
- logger::log_debug("srv_snapshot_manager_panel initializing")
+ data_load_status = reactive("ok"),
|
|||
| 102 | -77x - | +|||
| 173 | +
- setBookmarkExclude(c("show_snapshot_manager"))
- |
- |||
| 103 | -77x - | -
- observeEvent(input$show_snapshot_manager, {
+ is_active = reactive(TRUE)) {
|
||
| 104 | -! | -
- logger::log_debug("srv_snapshot_manager_panel@1 show_snapshot_manager button has been clicked.")
- |
- ||
| 105 | +174 | ! |
- showModal(+ stop("Modules class not supported: ", paste(class(modules), collapse = " "))
|
|
| 106 | -! | +|||
| 175 | +
- modalDialog(+ } |
|||
| 107 | -! | +|||
| 176 | +
- ui_snapshot_manager(session$ns("module")),
+
|
|||
| 108 | -! | +|||
| 177 | +
- class = "snapshot_manager_modal",+ #' @rdname module_teal_module |
|||
| 109 | -! | +|||
| 178 | +
- size = "m",+ #' @export |
|||
| 110 | -! | +|||
| 179 | +
- footer = NULL,+ srv_teal_module.teal_modules <- function(id, |
|||
| 111 | -! | +|||
| 180 | +
- easyClose = TRUE+ data_rv, |
|||
| 112 | +181 |
- )+ modules, |
||
| 113 | +182 |
- )+ datasets = NULL, |
||
| 114 | +183 |
- })+ slices_global, |
||
| 115 | -77x - | +|||
| 184 | +
- srv_snapshot_manager("module", slices_global = slices_global)
+ reporter = teal.reporter::Reporter$new(), |
|||
| 116 | +185 |
- })+ data_load_status = reactive("ok"),
|
||
| 117 | +186 |
- }+ is_active = reactive(TRUE)) {
|
||
| 118 | -+ | |||
| 187 | +80x |
-
+ moduleServer(id = id, module = function(input, output, session) {
|
||
| 119 | -+ | |||
| 188 | +80x |
- #' @rdname module_snapshot_manager+ logger::log_debug("srv_teal_module.teal_modules initializing the module { deparse1(modules$label) }.")
|
||
| 120 | +189 |
- ui_snapshot_manager <- function(id) {
+
|
||
| 121 | -! | +|||
| 190 | +80x |
- ns <- NS(id)+ observeEvent(data_load_status(), {
|
||
| 122 | -! | +|||
| 191 | +73x |
- tags$div(+ tabs_selector <- sprintf("#%s li a", session$ns("active_tab"))
|
||
| 123 | -! | +|||
| 192 | +73x |
- class = "manager_content",+ if (identical(data_load_status(), "ok")) {
|
||
| 124 | -! | +|||
| 193 | +68x |
- tags$div(+ logger::log_debug("srv_teal_module@1 enabling modules tabs.")
|
||
| 125 | -! | +|||
| 194 | +68x |
- class = "manager_table_row",+ shinyjs::show("wrapper")
|
||
| 126 | -! | +|||
| 195 | +68x |
- tags$span(tags$b("Snapshot manager")),
+ shinyjs::enable(selector = tabs_selector) |
||
| 127 | -! | +|||
| 196 | +5x |
- actionLink(ns("snapshot_add"), label = NULL, icon = icon("fas fa-camera"), title = "add snapshot"),
+ } else if (identical(data_load_status(), "teal_data_module failed")) {
|
||
| 128 | -! | +|||
| 197 | +5x |
- actionLink(ns("snapshot_load"), label = NULL, icon = icon("fas fa-upload"), title = "upload snapshot"),
+ logger::log_debug("srv_teal_module@1 disabling modules tabs.")
|
||
| 129 | -! | +|||
| 198 | +5x |
- actionLink(ns("snapshot_reset"), label = NULL, icon = icon("fas fa-undo"), title = "reset initial state"),
+ shinyjs::disable(selector = tabs_selector) |
||
| 130 | +199 | ! |
- NULL+ } else if (identical(data_load_status(), "external failed")) {
|
|
| 131 | -+ | |||
| 200 | +! |
- ),+ logger::log_debug("srv_teal_module@1 hiding modules tabs.")
|
||
| 132 | +201 | ! |
- uiOutput(ns("snapshot_list"))
+ shinyjs::hide("wrapper")
|
|
| 133 | +202 |
- )+ } |
||
| 134 | +203 |
- }+ }) |
||
| 135 | +204 | |||
| 136 | -+ | |||
| 205 | +80x |
- #' @rdname module_snapshot_manager+ modules_output <- sapply( |
||
| 137 | -+ | |||
| 206 | +80x |
- srv_snapshot_manager <- function(id, slices_global) {
+ names(modules$children), |
||
| 138 | -77x - | +207 | +80x |
- checkmate::assert_character(id)+ function(module_id) {
|
| 139 | -+ | |||
| 208 | +105x |
-
+ srv_teal_module( |
||
| 140 | -77x - | +209 | +105x |
- moduleServer(id, function(input, output, session) {
+ id = module_id, |
| 141 | -77x - | +210 | +105x |
- logger::log_debug("srv_snapshot_manager initializing")
+ data_rv = data_rv, |
| 142 | -+ | |||
| 211 | +105x |
-
+ modules = modules$children[[module_id]], |
||
| 143 | -+ | |||
| 212 | +105x |
- # Set up bookmarking callbacks ----+ datasets = datasets, |
||
| 144 | -+ | |||
| 213 | +105x |
- # Register bookmark exclusions (all buttons and text fields).+ slices_global = slices_global, |
||
| 145 | -77x - | +214 | +105x |
- setBookmarkExclude(c(+ reporter = reporter, |
| 146 | -77x - | +215 | +105x |
- "snapshot_add", "snapshot_load", "snapshot_reset",+ is_active = reactive( |
| 147 | -77x - | +216 | +105x |
- "snapshot_name_accept", "snaphot_file_accept",+ is_active() && |
| 148 | -77x - | +217 | +105x |
- "snapshot_name", "snapshot_file"+ input$active_tab == module_id && |
| 149 | -+ | |||
| 218 | +105x |
- ))+ identical(data_load_status(), "ok") |
||
| 150 | +219 |
- # Add snapshot history to bookmark.- |
- ||
| 151 | -77x - | -
- session$onBookmark(function(state) {
- |
- ||
| 152 | -! | -
- logger::log_debug("srv_snapshot_manager@onBookmark: storing snapshot and bookmark history")
- |
- ||
| 153 | -! | -
- state$values$snapshot_history <- snapshot_history() # isolate this?+ ) |
||
| 154 | +220 |
- })+ ) |
||
| 155 | +221 |
-
+ }, |
||
| 156 | -77x - | +222 | +80x |
- ns <- session$ns+ simplify = FALSE |
| 157 | +223 |
-
+ ) |
||
| 158 | +224 |
- # Track global filter states ----+ |
||
| 159 | -77x - | +225 | +80x |
- snapshot_history <- reactiveVal({
+ modules_output |
| 160 | +226 |
- # Restore directly from bookmarked state, if applicable.- |
- ||
| 161 | -77x - | -
- restoreValue(- |
- ||
| 162 | -77x - | -
- ns("snapshot_history"),
- |
- ||
| 163 | -77x - | -
- list("Initial application state" = shiny::isolate(as.list(slices_global$all_slices(), recursive = TRUE)))
+ }) |
||
| 164 | +227 |
- )+ } |
||
| 165 | +228 |
- })+ |
||
| 166 | +229 |
-
+ #' @rdname module_teal_module |
||
| 167 | +230 |
- # Snapshot current application state ----+ #' @export |
||
| 168 | +231 |
- # Name snaphsot.- |
- ||
| 169 | -77x - | -
- observeEvent(input$snapshot_add, {
- |
- ||
| 170 | -! | -
- logger::log_debug("srv_snapshot_manager: snapshot_add button clicked")
- |
- ||
| 171 | -! | -
- showModal(- |
- ||
| 172 | -! | -
- modalDialog(- |
- ||
| 173 | -! | -
- textInput(ns("snapshot_name"), "Name the snapshot", width = "100%", placeholder = "Meaningful, unique name"),
- |
- ||
| 174 | -! | -
- footer = tagList(- |
- ||
| 175 | -! | -
- actionButton(ns("snapshot_name_accept"), "Accept", icon = icon("far fa-thumbs-up")),
+ srv_teal_module.teal_module <- function(id, |
||
| 176 | -! | +|||
| 232 | +
- modalButton(label = "Cancel", icon = icon("far fa-thumbs-down"))
+ data_rv, |
|||
| 177 | +233 |
- ),+ modules, |
||
| 178 | -! | +|||
| 234 | +
- size = "s"+ datasets = NULL, |
|||
| 179 | +235 |
- )+ slices_global, |
||
| 180 | +236 |
- )+ reporter = teal.reporter::Reporter$new(), |
||
| 181 | +237 |
- })+ data_load_status = reactive("ok"),
|
||
| 182 | +238 |
- # Store snaphsot.+ is_active = reactive(TRUE)) {
|
||
| 183 | -77x - | -
- observeEvent(input$snapshot_name_accept, {
- |
- ||
| 184 | -! | -
- logger::log_debug("srv_snapshot_manager: snapshot_name_accept button clicked")
- |
- ||
| 185 | -! | +239 | +105x |
- snapshot_name <- trimws(input$snapshot_name)+ logger::log_debug("srv_teal_module.teal_module initializing the module: { deparse1(modules$label) }.")
|
| 186 | -! | +|||
| 240 | +105x |
- if (identical(snapshot_name, "")) {
+ moduleServer(id = id, module = function(input, output, session) {
|
||
| 187 | -! | +|||
| 241 | +105x |
- logger::log_debug("srv_snapshot_manager: snapshot name rejected")
+ module_out <- reactiveVal() |
||
| 188 | -! | +|||
| 242 | +
- showNotification(+ |
|||
| 189 | -! | +|||
| 243 | +105x |
- "Please name the snapshot.",+ active_datanames <- reactive({
|
||
| 190 | -! | +|||
| 244 | +82x |
- type = "message"+ .resolve_module_datanames(data = data_rv(), modules = modules) |
||
| 191 | +245 |
- )- |
- ||
| 192 | -! | -
- updateTextInput(inputId = "snapshot_name", value = "", placeholder = "Meaningful, unique name")+ }) |
||
| 193 | -! | +|||
| 246 | +105x |
- } else if (is.element(make.names(snapshot_name), make.names(names(snapshot_history())))) {
+ if (is.null(datasets)) {
|
||
| 194 | -! | +|||
| 247 | +20x |
- logger::log_debug("srv_snapshot_manager: snapshot name rejected")
+ datasets <- eventReactive(data_rv(), {
|
||
| 195 | -! | +|||
| 248 | +16x |
- showNotification(+ req(inherits(data_rv(), "teal_data")) |
||
| 196 | -! | +|||
| 249 | +16x |
- "This name is in conflict with other snapshot names. Please choose a different one.",+ logger::log_debug("srv_teal_module@1 initializing module-specific FilteredData")
|
||
| 197 | -! | +|||
| 250 | +16x |
- type = "message"+ teal_data_to_filtered_data(data_rv(), datanames = active_datanames()) |
||
| 198 | +251 |
- )- |
- ||
| 199 | -! | -
- updateTextInput(inputId = "snapshot_name", value = "", placeholder = "Meaningful, unique name")+ }) |
||
| 200 | +252 |
- } else {
- |
- ||
| 201 | -! | -
- logger::log_debug("srv_snapshot_manager: snapshot name accepted, adding snapshot")
- |
- ||
| 202 | -! | -
- snapshot <- as.list(slices_global$all_slices(), recursive = TRUE)- |
- ||
| 203 | -! | -
- snapshot_update <- c(snapshot_history(), list(snapshot))- |
- ||
| 204 | -! | -
- names(snapshot_update)[length(snapshot_update)] <- snapshot_name+ } |
||
| 205 | -! | +|||
| 253 | +
- snapshot_history(snapshot_update)+ |
|||
| 206 | -! | +|||
| 254 | +
- removeModal()+ # manage module filters on the module level |
|||
| 207 | +255 |
- # Reopen filter manager modal by clicking button in the main application.+ # important: |
||
| 208 | -! | +|||
| 256 | +
- shinyjs::click(id = "teal-wunder_bar-show_snapshot_manager", asis = TRUE)+ # filter_manager_module_srv needs to be called before filter_panel_srv |
|||
| 209 | +257 |
- }+ # Because available_teal_slices is used in FilteredData$srv_available_slices (via srv_filter_panel) |
||
| 210 | +258 |
- })+ # and if it is not set, then it won't be available in the srv_filter_panel |
||
| 211 | -+ | |||
| 259 | +105x |
-
+ srv_module_filter_manager(modules$label, module_fd = datasets, slices_global = slices_global) |
||
| 212 | +260 |
- # Upload a snapshot file ----+ |
||
| 213 | -+ | |||
| 261 | +105x |
- # Select file.+ call_once_when(is_active(), {
|
||
| 214 | -77x - | +262 | +79x |
- observeEvent(input$snapshot_load, {
+ filtered_teal_data <- srv_filter_data( |
| 215 | -! | +|||
| 263 | +79x |
- logger::log_debug("srv_snapshot_manager: snapshot_load button clicked")
+ "filter_panel", |
||
| 216 | -! | +|||
| 264 | +79x |
- showModal(+ datasets = datasets, |
||
| 217 | -! | +|||
| 265 | +79x |
- modalDialog(+ active_datanames = active_datanames, |
||
| 218 | -! | +|||
| 266 | +79x |
- fileInput(ns("snapshot_file"), "Choose snapshot file", accept = ".json", width = "100%"),
+ data_rv = data_rv, |
||
| 219 | -! | +|||
| 267 | +79x |
- textInput(+ is_active = is_active |
||
| 220 | -! | +|||
| 268 | +
- ns("snapshot_name"),
+ ) |
|||
| 221 | -! | +|||
| 269 | +79x |
- "Name the snapshot (optional)",+ is_transformer_failed <- reactiveValues() |
||
| 222 | -! | +|||
| 270 | +79x |
- width = "100%",+ transformed_teal_data <- srv_transform_data( |
||
| 223 | -! | +|||
| 271 | +79x |
- placeholder = "Meaningful, unique name"+ "data_transform", |
||
| 224 | -+ | |||
| 272 | +79x |
- ),+ data = filtered_teal_data, |
||
| 225 | -! | +|||
| 273 | +79x |
- footer = tagList(+ transformers = modules$transformers, |
||
| 226 | -! | +|||
| 274 | +79x |
- actionButton(ns("snaphot_file_accept"), "Accept", icon = icon("far fa-thumbs-up")),
+ modules = modules, |
||
| 227 | -! | +|||
| 275 | +79x |
- modalButton(label = "Cancel", icon = icon("far fa-thumbs-down"))
+ is_transformer_failed = is_transformer_failed |
||
| 228 | +276 |
- )+ ) |
||
| 229 | -+ | |||
| 277 | +79x |
- )+ any_transformer_failed <- reactive({
|
||
| 230 | -+ | |||
| 278 | +79x |
- )+ any(unlist(reactiveValuesToList(is_transformer_failed))) |
||
| 231 | +279 |
- })+ }) |
||
| 232 | +280 |
- # Store new snapshot to list and restore filter states.+ |
||
| 233 | -77x - | -
- observeEvent(input$snaphot_file_accept, {
- |
- ||
| 234 | -! | +281 | +79x |
- logger::log_debug("srv_snapshot_manager: snapshot_file_accept button clicked")
+ observeEvent(any_transformer_failed(), {
|
| 235 | -! | +|||
| 282 | +79x |
- snapshot_name <- trimws(input$snapshot_name)+ if (isTRUE(any_transformer_failed())) {
|
||
| 236 | -! | +|||
| 283 | +6x |
- if (identical(snapshot_name, "")) {
+ shinyjs::hide("teal_module_ui")
|
||
| 237 | -! | +|||
| 284 | +6x |
- logger::log_debug("srv_snapshot_manager: no snapshot name provided, naming after file")
+ shinyjs::hide("validate_datanames")
|
||
| 238 | -! | +|||
| 285 | +6x |
- snapshot_name <- tools::file_path_sans_ext(input$snapshot_file$name)+ shinyjs::show("transformer_failure_info")
|
||
| 239 | +286 |
- }- |
- ||
| 240 | -! | -
- if (is.element(make.names(snapshot_name), make.names(names(snapshot_history())))) {
- |
- ||
| 241 | -! | -
- logger::log_debug("srv_snapshot_manager: snapshot name rejected")
+ } else {
|
||
| 242 | -! | +|||
| 287 | +73x |
- showNotification(+ shinyjs::show("teal_module_ui")
|
||
| 243 | -! | +|||
| 288 | +73x |
- "This name is in conflict with other snapshot names. Please choose a different one.",+ shinyjs::show("validate_datanames")
|
||
| 244 | -! | +|||
| 289 | +73x |
- type = "message"+ shinyjs::hide("transformer_failure_info")
|
||
| 245 | +290 |
- )+ } |
||
| 246 | -! | +|||
| 291 | +
- updateTextInput(inputId = "snapshot_name", value = "", placeholder = "Meaningful, unique name")+ }) |
|||
| 247 | +292 |
- } else {
+
|
||
| 248 | -+ | |||
| 293 | +79x |
- # Restore snapshot and verify app compatibility.+ module_teal_data <- reactive({
|
||
| 249 | -! | +|||
| 294 | +87x |
- logger::log_debug("srv_snapshot_manager: snapshot name accepted, loading snapshot")
+ req(inherits(transformed_teal_data(), "teal_data")) |
||
| 250 | -! | +|||
| 295 | +81x |
- snapshot_state <- try(slices_restore(input$snapshot_file$datapath))+ all_teal_data <- transformed_teal_data() |
||
| 251 | -! | +|||
| 296 | +81x |
- if (!inherits(snapshot_state, "modules_teal_slices")) {
+ module_datanames <- .resolve_module_datanames(data = all_teal_data, modules = modules) |
||
| 252 | -! | +|||
| 297 | +81x |
- logger::log_debug("srv_snapshot_manager: snapshot file corrupt")
+ .subset_teal_data(all_teal_data, module_datanames) |
||
| 253 | -! | +|||
| 298 | +
- showNotification(+ }) |
|||
| 254 | -! | +|||
| 299 | +
- "File appears to be corrupt.",+ |
|||
| 255 | -! | +|||
| 300 | +79x |
- type = "error"+ srv_validate_reactive_teal_data( |
||
| 256 | -+ | |||
| 301 | +79x |
- )+ "validate_datanames", |
||
| 257 | -! | +|||
| 302 | +79x |
- } else if (!identical(attr(snapshot_state, "app_id"), attr(slices_global$all_slices(), "app_id"))) {
+ data = module_teal_data, |
||
| 258 | -! | +|||
| 303 | +79x |
- logger::log_debug("srv_snapshot_manager: snapshot not compatible with app")
+ modules = modules |
||
| 259 | -! | +|||
| 304 | +
- showNotification(+ ) |
|||
| 260 | -! | +|||
| 305 | +
- "This snapshot file is not compatible with the app and cannot be loaded.",+ |
|||
| 261 | -! | +|||
| 306 | +79x |
- type = "warning"+ summary_table <- srv_data_summary("data_summary", module_teal_data)
|
||
| 262 | +307 |
- )+ |
||
| 263 | +308 |
- } else {
+ # Call modules. |
||
| 264 | -+ | |||
| 309 | +79x |
- # Add to snapshot history.+ if (!inherits(modules, "teal_module_previewer")) {
|
||
| 265 | -! | +|||
| 310 | +79x |
- logger::log_debug("srv_snapshot_manager: snapshot loaded, adding to history")
+ obs_module <- call_once_when( |
||
| 266 | -! | +|||
| 311 | +79x |
- snapshot <- as.list(slices_global$all_slices(), recursive = TRUE)+ !is.null(module_teal_data()), |
||
| 267 | -! | +|||
| 312 | +79x |
- snapshot_update <- c(snapshot_history(), list(snapshot))+ ignoreNULL = TRUE, |
||
| 268 | -! | +|||
| 313 | +79x |
- names(snapshot_update)[length(snapshot_update)] <- snapshot_name+ handlerExpr = {
|
||
| 269 | -! | +|||
| 314 | +73x |
- snapshot_history(snapshot_update)+ module_out(.call_teal_module(modules, datasets, module_teal_data, reporter)) |
||
| 270 | +315 |
- ### Begin simplified restore procedure. ###+ } |
||
| 271 | -! | +|||
| 316 | +
- logger::log_debug("srv_snapshot_manager: restoring snapshot")
+ ) |
|||
| 272 | -! | +|||
| 317 | +
- slices_global$slices_set(snapshot_state)+ } else {
|
|||
| 273 | -! | +|||
| 318 | +
- removeModal()+ # Report previewer must be initiated on app start for report cards to be included in bookmarks. |
|||
| 274 | +319 |
- ### End simplified restore procedure. ###+ # When previewer is delayed, cards are bookmarked only if previewer has been initiated (visited). |
||
| 275 | -+ | |||
| 320 | +! |
- }+ module_out(.call_teal_module(modules, datasets, module_teal_data, reporter)) |
||
| 276 | +321 |
} |
||
| 277 | +322 |
- })+ |
||
| 278 | +323 |
- # Apply newly added snapshot.+ # todo: (feature request) add a ReporterCard to the reporter as an output from the teal_module |
||
| 279 | +324 |
-
+ # how to determine if module returns a ReporterCard so that reportPreviewer is needed? |
||
| 280 | +325 |
- # Restore initial state ----- |
- ||
| 281 | -77x - | -
- observeEvent(input$snapshot_reset, {
+ # Should we insertUI of the ReportPreviewer then? |
||
| 282 | -2x - | +|||
| 326 | +
- logger::log_debug("srv_snapshot_manager: snapshot_reset button clicked, restoring snapshot")
+ # What about attr(module, "reportable") - similar to attr(module, "bookmarkable") |
|||
| 283 | -2x - | +327 | +79x |
- s <- "Initial application state"+ if ("report" %in% names(module_out)) {
|
| 284 | +328 |
- ### Begin restore procedure. ###- |
- ||
| 285 | -2x - | -
- snapshot <- snapshot_history()[[s]]+ # (reactively) add card to the reporter |
||
| 286 | +329 |
- # todo: as.teal_slices looses module-mapping if is not global+ } |
||
| 287 | -2x - | +|||
| 330 | +
- snapshot_state <- as.teal_slices(snapshot)+ }) |
|||
| 288 | -2x - | +|||
| 331 | +
- slices_global$slices_set(snapshot_state)+ |
|||
| 289 | -2x - | +332 | +105x |
- removeModal()+ module_out |
| 290 | +333 |
- ### End restore procedure. ###+ }) |
||
| 291 | +334 |
- })+ } |
||
| 292 | +335 | |||
| 293 | +336 |
- # Build snapshot table ----+ # This function calls a module server function. |
||
| 294 | +337 |
- # Create UI elements and server logic for the snapshot table.+ .call_teal_module <- function(modules, datasets, filtered_teal_data, reporter) {
|
||
| 295 | +338 |
- # Observers must be tracked to avoid duplication and excess reactivity.+ # collect arguments to run teal_module |
||
| 296 | -+ | |||
| 339 | +73x |
- # Remaining elements are tracked likewise for consistency and a slight speed margin.+ args <- c(list(id = "module"), modules$server_args) |
||
| 297 | -77x - | +340 | +73x |
- observers <- reactiveValues()+ if (is_arg_used(modules$server, "reporter")) {
|
| 298 | -77x - | +341 | +1x |
- handlers <- reactiveValues()+ args <- c(args, list(reporter = reporter)) |
| 299 | -77x - | +|||
| 342 | +
- divs <- reactiveValues()+ } |
|||
| 300 | +343 | |||
| 301 | -77x - | +344 | +73x |
- observeEvent(snapshot_history(), {
+ if (is_arg_used(modules$server, "datasets")) {
|
| 302 | -67x - | +345 | +1x |
- logger::log_debug("srv_snapshot_manager: snapshot history modified, updating snapshot list")
+ args <- c(args, datasets = datasets()) |
| 303 | -67x - | +346 | +1x |
- lapply(names(snapshot_history())[-1L], function(s) {
+ warning("datasets argument is not reactive and therefore it won't be updated when data is refreshed.")
|
| 304 | -! | +|||
| 347 | +
- id_pickme <- sprintf("pickme_%s", make.names(s))
+ } |
|||
| 305 | -! | +|||
| 348 | +
- id_saveme <- sprintf("saveme_%s", make.names(s))
+
|
|||
| 306 | -! | +|||
| 349 | +73x |
- id_rowme <- sprintf("rowme_%s", make.names(s))
+ if (is_arg_used(modules$server, "data")) {
+ |
+ ||
| 350 | +69x | +
+ args <- c(args, data = list(filtered_teal_data)) |
||
| 307 | +351 |
-
+ } |
||
| 308 | +352 |
- # Observer for restoring snapshot.+ |
||
| 309 | -! | +|||
| 353 | +73x |
- if (!is.element(id_pickme, names(observers))) {
+ if (is_arg_used(modules$server, "filter_panel_api")) {
|
||
| 310 | -! | +|||
| 354 | +1x |
- observers[[id_pickme]] <- observeEvent(input[[id_pickme]], {
+ args <- c(args, filter_panel_api = teal.slice::FilterPanelAPI$new(datasets())) |
||
| 311 | +355 |
- ### Begin restore procedure. ###+ } |
||
| 312 | -! | +|||
| 356 | +
- snapshot <- snapshot_history()[[s]]+ |
|||
| 313 | -! | +|||
| 357 | +73x |
- snapshot_state <- as.teal_slices(snapshot)+ if (is_arg_used(modules$server, "id")) {
|
||
| 314 | -+ | |||
| 358 | +73x |
-
+ do.call(modules$server, args) |
||
| 315 | -! | +|||
| 359 | +
- slices_global$slices_set(snapshot_state)+ } else {
|
|||
| 316 | +360 | ! |
- removeModal()+ do.call(callModule, c(args, list(module = modules$server))) |
|
| 317 | +361 |
- ### End restore procedure. ###+ } |
||
| 318 | +362 |
- })+ } |
||
| 319 | +363 |
- }+ |
||
| 320 | +364 |
- # Create handler for downloading snapshot.+ .resolve_module_datanames <- function(data, modules) {
|
||
| 321 | -! | +|||
| 365 | +163x |
- if (!is.element(id_saveme, names(handlers))) {
+ stopifnot("data_rv must be teal_data object." = inherits(data, "teal_data"))
|
||
| 322 | -! | +|||
| 366 | +163x |
- output[[id_saveme]] <- downloadHandler(+ if (is.null(modules$datanames) || identical(modules$datanames, "all")) {
|
||
| 323 | -! | +|||
| 367 | +131x |
- filename = function() {
+ .topologically_sort_datanames(ls(teal.code::get_env(data)), teal.data::join_keys(data)) |
||
| 324 | -! | +|||
| 368 | +
- sprintf("teal_snapshot_%s_%s.json", s, Sys.Date())
+ } else {
+ |
+ |||
| 369 | +32x | +
+ intersect(+ |
+ ||
| 370 | +32x | +
+ .include_parent_datanames(modules$datanames, teal.data::join_keys(data)),+ |
+ ||
| 371 | +32x | +
+ ls(teal.code::get_env(data)) |
||
| 325 | +372 |
- },+ ) |
||
| 326 | -! | +|||
| 373 | +
- content = function(file) {
+ } |
|||
| 327 | -! | +|||
| 374 | +
- snapshot <- snapshot_history()[[s]]+ } |
|||
| 328 | -! | +|||
| 375 | +
- snapshot_state <- as.teal_slices(snapshot)+ |
|||
| 329 | -! | +|||
| 376 | +
- slices_store(tss = snapshot_state, file = file)+ #' Calls expression when condition is met |
|||
| 330 | +377 |
- }+ #' |
||
| 331 | +378 |
- )+ #' Function postpones `handlerExpr` to the moment when `eventExpr` (condition) returns `TRUE`, |
||
| 332 | -! | +|||
| 379 | +
- handlers[[id_saveme]] <- id_saveme+ #' otherwise nothing happens. |
|||
| 333 | +380 |
- }+ #' @param eventExpr A (quoted or unquoted) logical expression that represents the event; |
||
| 334 | +381 |
- # Create a row for the snapshot table.+ #' this can be a simple reactive value like input$click, a call to a reactive expression |
||
| 335 | -! | +|||
| 382 | +
- if (!is.element(id_rowme, names(divs))) {
+ #' like dataset(), or even a complex expression inside curly braces. |
|||
| 336 | -! | +|||
| 383 | +
- divs[[id_rowme]] <- tags$div(+ #' @param ... additional arguments passed to `observeEvent` with the exception of `eventExpr` that is not allowed. |
|||
| 337 | -! | +|||
| 384 | +
- class = "manager_table_row",+ #' @inheritParams shiny::observeEvent |
|||
| 338 | -! | +|||
| 385 | +
- tags$span(tags$h5(s)),+ #' |
|||
| 339 | -! | +|||
| 386 | +
- actionLink(inputId = ns(id_pickme), label = icon("far fa-circle-check"), title = "select"),
+ #' @return An observer. |
|||
| 340 | -! | +|||
| 387 | +
- downloadLink(outputId = ns(id_saveme), label = icon("far fa-save"), title = "save to file")
+ #' |
|||
| 341 | +388 |
- )+ #' @keywords internal |
||
| 342 | +389 |
- }+ call_once_when <- function(eventExpr, # nolint: object_name. |
||
| 343 | +390 |
- })+ handlerExpr, # nolint: object_name. |
||
| 344 | +391 |
- })+ event.env = parent.frame(), # nolint: object_name. |
||
| 345 | +392 |
-
+ handler.env = parent.frame(), # nolint: object_name. |
||
| 346 | +393 |
- # Create table to display list of snapshots and their actions.+ ...) {
|
||
| 347 | -77x - | +394 | +184x |
- output$snapshot_list <- renderUI({
+ event_quo <- rlang::new_quosure(substitute(eventExpr), env = event.env) |
| 348 | -67x - | +395 | +184x |
- rows <- rev(reactiveValuesToList(divs))+ handler_quo <- rlang::new_quosure(substitute(handlerExpr), env = handler.env) |
| 349 | -67x - | +|||
| 396 | +
- if (length(rows) == 0L) {
+
+ |
+ |||
| 397 | ++ |
+ # When `condExpr` is TRUE, then `handlerExpr` is evaluated once. |
||
| 350 | -67x - | +398 | +184x |
- tags$div(+ activator <- reactive({
|
| 351 | -67x - | +399 | +184x |
- class = "manager_placeholder",+ if (isTRUE(rlang::eval_tidy(event_quo))) {
|
| 352 | -67x - | +400 | +152x |
- "Snapshots will appear here."+ TRUE |
| 353 | +401 |
- )+ } |
||
| 354 | +402 |
- } else {
+ }) |
||
| 355 | -! | +|||
| 403 | +
- rows+ |
|||
| 356 | -+ | |||
| 404 | +184x |
- }+ observeEvent( |
||
| 357 | -+ | |||
| 405 | +184x |
- })+ eventExpr = activator(), |
||
| 358 | -+ | |||
| 406 | +184x |
-
+ once = TRUE, |
||
| 359 | -77x - | +407 | +184x |
- snapshot_history+ handlerExpr = rlang::eval_tidy(handler_quo), |
| 360 | +408 |
- })+ ... |
||
| 361 | +409 | ++ |
+ )+ |
+ |
| 410 |
}@@ -23058,14 +21348,14 @@ teal coverage - 59.73% |
| 1 |
- #' App state management.+ #' Send input validation messages to output |
|||
| 3 |
- #' @description+ #' Captures messages from `InputValidator` objects and collates them |
|||
| 4 |
- #' `r lifecycle::badge("experimental")`
+ #' into one message passed to `validate`. |
|||
| 6 |
- #' Capture and restore the global (app) input state.+ #' `shiny::validate` is used to withhold rendering of an output element until |
|||
| 7 |
- #'+ #' certain conditions are met and to print a validation message in place |
|||
| 8 |
- #' @details+ #' of the output element. |
|||
| 9 |
- #' This module introduces bookmarks into `teal` apps: the `shiny` bookmarking mechanism becomes enabled+ #' `shinyvalidate::InputValidator` allows to validate input elements |
|||
| 10 |
- #' and server-side bookmarks can be created.+ #' and to display specific messages in their respective input widgets. |
|||
| 11 |
- #'+ #' `validate_inputs` provides a hybrid solution. |
|||
| 12 |
- #' The bookmark manager presents a button with the bookmark icon and is placed in the tab-bar.+ #' Given an `InputValidator` object, messages corresponding to inputs that fail validation |
|||
| 13 |
- #' When clicked, the button creates a bookmark and opens a modal which displays the bookmark URL.+ #' 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 |
- #' `teal` does not guarantee that all modules (`teal_module` objects) are bookmarkable.+ #' |
|||
| 16 |
- #' Those that are, have a `teal_bookmarkable` attribute set to `TRUE`. If any modules are not bookmarkable,+ #' The `...` argument accepts any number of `InputValidator` objects |
|||
| 17 |
- #' the bookmark manager modal displays a warning and the bookmark button displays a flag.+ #' or a nested list of such objects. |
|||
| 18 |
- #' In order to communicate that a external module is bookmarkable, the module developer+ #' If `validators` are passed directly, all their messages are printed together |
|||
| 19 |
- #' should set the `teal_bookmarkable` attribute to `TRUE`.+ #' 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 |
- #' @section Server logic:+ #' for their respective message groups. |
|||
| 22 |
- #' A bookmark is a URL that contains the app address with a `/?_state_id_=<bookmark_dir>` suffix.+ #' If neither of the nested list elements is named, a header message is taken from `header`. |
|||
| 23 |
- #' `<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.+ #' @param ... either any number of `InputValidator` objects |
|||
| 25 |
- #'+ #' or an optionally named, possibly nested `list` of `InputValidator` |
|||
| 26 |
- #' @section Note:+ #' objects, see `Details` |
|||
| 27 |
- #' To enable bookmarking use either:+ #' @param header (`character(1)`) generic validation message; set to NULL to omit |
|||
| 28 |
- #' - `shiny` app by using `shinyApp(..., enableBookmarking = "server")` (not supported in `shinytest2`)+ #' |
|||
| 29 |
- #' - set `options(shiny.bookmarkStore = "server")` before running the app+ #' @return |
|||
| 30 |
- #'+ #' Returns NULL if the final validation call passes and a `shiny.silent.error` if it fails. |
|||
| 32 |
- #' @inheritParams init+ #' @seealso [`shinyvalidate::InputValidator`], [`shiny::validate`] |
|||
| 34 |
- #' @return Invisible `NULL`.+ #' @examplesIf require("shinyvalidate")
|
|||
| 35 |
- #'+ #' library(shiny) |
|||
| 36 |
- #' @aliases bookmark bookmark_manager bookmark_manager_module+ #' library(shinyvalidate) |
|||
| 38 |
- #' @name module_bookmark_manager+ #' ui <- fluidPage( |
|||
| 39 |
- #' @rdname module_bookmark_manager+ #' selectInput("method", "validation method", c("sequential", "combined", "grouped")),
|
|||
| 40 |
- #'+ #' sidebarLayout( |
|||
| 41 |
- #' @keywords internal+ #' sidebarPanel( |
|||
| 42 |
- #'+ #' selectInput("letter", "select a letter:", c(letters[1:3], LETTERS[4:6])),
|
|||
| 43 |
- NULL+ #' selectInput("number", "select a number:", 1:6),
|
|||
| 44 |
-
+ #' tags$br(), |
|||
| 45 |
- #' @rdname module_bookmark_manager+ #' selectInput("color", "select a color:",
|
|||
| 46 |
- ui_bookmark_panel <- function(id, modules) {
+ #' c("black", "indianred2", "springgreen2", "cornflowerblue"),
|
|||
| 47 | -! | +
- ns <- NS(id)+ #' multiple = TRUE |
||
| 48 |
-
+ #' ), |
|||
| 49 | -! | +
- bookmark_option <- get_bookmarking_option()+ #' sliderInput("size", "select point size:",
|
||
| 50 | -! | +
- is_unbookmarkable <- need_bookmarking(modules)+ #' min = 0.1, max = 4, value = 0.25 |
||
| 51 | -! | +
- shinyOptions(bookmarkStore = bookmark_option)+ #' ) |
||
| 52 |
-
+ #' ), |
|||
| 53 |
- # Render bookmark warnings count+ #' mainPanel(plotOutput("plot"))
|
|||
| 54 | -! | +
- if (!all(is_unbookmarkable) && identical(bookmark_option, "server")) {
+ #' ) |
||
| 55 | -! | +
- tags$button(+ #' ) |
||
| 56 | -! | +
- id = ns("do_bookmark"),
+ #' |
||
| 57 | -! | +
- class = "btn action-button wunder_bar_button bookmark_manager_button",+ #' server <- function(input, output) {
|
||
| 58 | -! | +
- title = "Add bookmark",+ #' # set up input validation |
||
| 59 | -! | +
- tags$span(+ #' iv <- InputValidator$new() |
||
| 60 | -! | +
- suppressMessages(icon("fas fa-bookmark")),
+ #' iv$add_rule("letter", sv_in_set(LETTERS, "choose a capital letter"))
|
||
| 61 | -! | +
- if (any(is_unbookmarkable)) {
+ #' iv$add_rule("number", function(x) {
|
||
| 62 | -! | +
- tags$span(+ #' if (as.integer(x) %% 2L == 1L) "choose an even number" |
||
| 63 | -! | +
- sum(is_unbookmarkable),+ #' })+ |
+ ||
| 64 | ++ |
+ #' iv$enable()+ |
+ ||
| 65 | ++ |
+ #' # more input validation+ |
+ ||
| 66 | ++ |
+ #' iv_par <- InputValidator$new()+ |
+ ||
| 67 | ++ |
+ #' iv_par$add_rule("color", sv_required(message = "choose a color"))
+ |
+ ||
| 68 | ++ |
+ #' iv_par$add_rule("color", function(x) {
+ |
+ ||
| 69 | ++ |
+ #' if (length(x) > 1L) "choose only one color"+ |
+ ||
| 70 | ++ |
+ #' })+ |
+ ||
| 71 | ++ |
+ #' iv_par$add_rule(+ |
+ ||
| 72 | ++ |
+ #' "size",+ |
+ ||
| 73 | ++ |
+ #' sv_between(+ |
+ ||
| 74 | ++ |
+ #' left = 0.5, right = 3,+ |
+ ||
| 75 | ++ |
+ #' message_fmt = "choose a value between {left} and {right}"
+ |
+ ||
| 76 | ++ |
+ #' )+ |
+ ||
| 77 | ++ |
+ #' )+ |
+ ||
| 78 | ++ |
+ #' iv_par$enable()+ |
+ ||
| 79 | ++ |
+ #'+ |
+ ||
| 80 | ++ |
+ #' output$plot <- renderPlot({
+ |
+ ||
| 81 | ++ |
+ #' # validate output+ |
+ ||
| 82 | ++ |
+ #' switch(input[["method"]],+ |
+ ||
| 83 | ++ |
+ #' "sequential" = {
+ |
+ ||
| 84 | ++ |
+ #' validate_inputs(iv)+ |
+ ||
| 85 | ++ |
+ #' validate_inputs(iv_par, header = "Set proper graphical parameters")+ |
+ ||
| 86 | ++ |
+ #' },+ |
+ ||
| 87 | ++ |
+ #' "combined" = validate_inputs(iv, iv_par),+ |
+ ||
| 88 | ++ |
+ #' "grouped" = validate_inputs(list(+ |
+ ||
| 89 | ++ |
+ #' "Some inputs require attention" = iv,+ |
+ ||
| 90 | ++ |
+ #' "Set proper graphical parameters" = iv_par+ |
+ ||
| 91 | ++ |
+ #' ))+ |
+ ||
| 92 | ++ |
+ #' )+ |
+ ||
| 93 | ++ |
+ #'+ |
+ ||
| 94 | ++ |
+ #' plot(faithful$eruptions ~ faithful$waiting,+ |
+ ||
| 95 | ++ |
+ #' las = 1, pch = 16,+ |
+ ||
| 96 | ++ |
+ #' col = input[["color"]], cex = input[["size"]]+ |
+ ||
| 97 | ++ |
+ #' ) |
||
| 64 | -! | +|||
| 98 | +
- class = "badge-warning badge-count text-white bg-danger"+ #' }) |
|||
| 65 | +99 |
- )+ #' } |
||
| 66 | +100 |
- }+ #' |
||
| 67 | +101 |
- )+ #' if (interactive()) {
|
||
| 68 | +102 |
- )+ #' shinyApp(ui, server) |
||
| 69 | +103 |
- }+ #' } |
||
| 70 | +104 |
- }+ #' |
||
| 71 | +105 |
-
+ #' @export |
||
| 72 | +106 |
- #' @rdname module_bookmark_manager+ #' |
||
| 73 | +107 |
- srv_bookmark_panel <- function(id, modules) {
+ validate_inputs <- function(..., header = "Some inputs require attention") {
|
||
| 74 | -77x - | +108 | +36x |
- checkmate::assert_character(id)+ dots <- list(...) |
| 75 | -77x - | +109 | +2x |
- checkmate::assert_class(modules, "teal_modules")+ if (!is_validators(dots)) stop("validate_inputs accepts validators or a list thereof")
|
| 76 | -77x - | +|||
| 110 | +
- moduleServer(id, function(input, output, session) {
+
|
|||
| 77 | -77x - | +111 | +34x |
- logger::log_debug("bookmark_manager_srv initializing")
+ messages <- extract_validator(dots, header) |
| 78 | -77x - | +112 | +34x |
- ns <- session$ns+ failings <- if (!any_names(dots)) {
|
| 79 | -77x - | +113 | +29x |
- bookmark_option <- get_bookmarking_option()+ add_header(messages, header)+ |
+
| 114 | ++ |
+ } else {
|
||
| 80 | -77x - | +115 | +5x |
- is_unbookmarkable <- need_bookmarking(modules)+ unlist(messages) |
| 81 | +116 | ++ |
+ }+ |
+ |
| 117 | ||||
| 118 | +34x | +
+ shiny::validate(shiny::need(is.null(failings), failings))+ |
+ ||
| 82 | +119 |
- # Set up bookmarking callbacks ----+ } |
||
| 83 | +120 |
- # Register bookmark exclusions: do_bookmark button to avoid re-bookmarking+ |
||
| 84 | -77x - | +|||
| 121 | +
- setBookmarkExclude(c("do_bookmark"))
+ ### internal functions |
|||
| 85 | +122 |
- # This bookmark can only be used on the app session.+ |
||
| 86 | -77x - | +|||
| 123 | +
- app_session <- .subset2(session, "parent")+ #' @noRd |
|||
| 87 | -77x - | +|||
| 124 | +
- app_session$onBookmarked(function(url) {
+ #' @keywords internal |
|||
| 88 | -! | +|||
| 125 | +
- logger::log_debug("bookmark_manager_srv@onBookmarked: bookmark button clicked, registering bookmark")
+ # recursive object type test |
|||
| 89 | -! | +|||
| 126 | +
- modal_content <- if (bookmark_option != "server") {
+ # returns logical of length 1 |
|||
| 90 | -! | +|||
| 127 | +
- msg <- sprintf(+ is_validators <- function(x) {
|
|||
| 91 | -! | +|||
| 128 | +118x |
- "Bookmarking has been set to \"%s\".\n%s\n%s",+ all(if (is.list(x)) unlist(lapply(x, is_validators)) else inherits(x, "InputValidator")) |
||
| 92 | -! | +|||
| 129 | +
- bookmark_option,+ } |
|||
| 93 | -! | +|||
| 130 | +
- "Only server-side bookmarking is supported.",+ |
|||
| 94 | -! | +|||
| 131 | +
- "Please contact your app developer."+ #' @noRd |
|||
| 95 | +132 |
- )+ #' @keywords internal |
||
| 96 | -! | +|||
| 133 | +
- tags$div(+ # test if an InputValidator object is enabled |
|||
| 97 | -! | +|||
| 134 | +
- tags$p(msg, class = "text-warning")+ # returns logical of length 1 |
|||
| 98 | +135 |
- )+ # official method requested at https://github.com/rstudio/shinyvalidate/issues/64 |
||
| 99 | +136 |
- } else {
+ validator_enabled <- function(x) {
|
||
| 100 | -! | +|||
| 137 | +49x |
- tags$div(+ x$.__enclos_env__$private$enabled |
||
| 101 | -! | +|||
| 138 | +
- tags$span(+ } |
|||
| 102 | -! | +|||
| 139 | +
- tags$pre(url)+ |
|||
| 103 | +140 |
- ),+ #' Recursively extract messages from validator list |
||
| 104 | -! | +|||
| 141 | +
- if (any(is_unbookmarkable)) {
+ #' @return A character vector or a list of character vectors, possibly nested and named. |
|||
| 105 | -! | +|||
| 142 | +
- bkmb_summary <- rapply2(+ #' @noRd |
|||
| 106 | -! | +|||
| 143 | +
- modules_bookmarkable(modules),+ #' @keywords internal |
|||
| 107 | -! | +|||
| 144 | +
- function(x) {
+ extract_validator <- function(iv, header) {
|
|||
| 108 | -! | +|||
| 145 | +113x |
- if (isTRUE(x)) {
+ if (inherits(iv, "InputValidator")) {
|
||
| 109 | -! | +|||
| 146 | +49x |
- "\u2705" # check mark+ add_header(gather_messages(iv), header) |
||
| 110 | -! | +|||
| 147 | +
- } else if (isFALSE(x)) {
+ } else {
|
|||
| 111 | -! | +|||
| 148 | +58x |
- "\u274C" # cross mark+ if (is.null(names(iv))) names(iv) <- rep("", length(iv))
+ |
+ ||
| 149 | +64x | +
+ mapply(extract_validator, iv = iv, header = names(iv), SIMPLIFY = FALSE) |
||
| 112 | +150 |
- } else {
+ } |
||
| 113 | -! | +|||
| 151 | +
- "\u2753" # question mark+ } |
|||
| 114 | +152 |
- }+ |
||
| 115 | +153 |
- }+ #' Collate failing messages from validator. |
||
| 116 | +154 |
- )+ #' @return `list` |
||
| 117 | -! | +|||
| 155 | +
- tags$div(+ #' @noRd |
|||
| 118 | -! | +|||
| 156 | +
- tags$p(+ #' @keywords internal |
|||
| 119 | -! | +|||
| 157 | +
- icon("fas fa-exclamation-triangle"),
+ gather_messages <- function(iv) {
|
|||
| 120 | -! | +|||
| 158 | +49x |
- "Some modules will not be restored when using this bookmark.",+ if (validator_enabled(iv)) {
|
||
| 121 | -! | +|||
| 159 | +46x |
- tags$br(),+ status <- iv$validate() |
||
| 122 | -! | +|||
| 160 | +46x |
- "Check the list below to see which modules are not bookmarkable.",+ failing_inputs <- Filter(Negate(is.null), status) |
||
| 123 | -! | +|||
| 161 | +46x |
- class = "text-warning"+ unique(lapply(failing_inputs, function(x) x[["message"]])) |
||
| 124 | +162 |
- ),+ } else {
|
||
| 125 | -! | +|||
| 163 | +3x |
- tags$pre(yaml::as.yaml(bkmb_summary))+ warning("Validator is disabled and will be omitted.")
+ |
+ ||
| 164 | +3x | +
+ list() |
||
| 126 | +165 |
- )+ } |
||
| 127 | +166 |
- }+ } |
||
| 128 | +167 |
- )+ |
||
| 129 | +168 |
- }+ #' Add optional header to failing messages |
||
| 130 | +169 |
-
+ #' @noRd |
||
| 131 | -! | +|||
| 170 | +
- showModal(+ #' @keywords internal |
|||
| 132 | -! | +|||
| 171 | +
- modalDialog(+ add_header <- function(messages, header = "") {
|
|||
| 133 | -! | +|||
| 172 | +78x |
- id = ns("bookmark_modal"),
+ ans <- unlist(messages) |
||
| 134 | -! | +|||
| 173 | +78x |
- title = "Bookmarked teal app url",+ if (length(ans) != 0L && isTRUE(nchar(header) > 0L)) {
|
||
| 135 | -! | +|||
| 174 | +31x |
- modal_content,+ ans <- c(paste0(header, "\n"), ans, "\n") |
||
| 136 | -! | +|||
| 175 | +
- easyClose = TRUE+ }+ |
+ |||
| 176 | +78x | +
+ ans |
||
| 137 | +177 |
- )+ } |
||
| 138 | +178 |
- )+ |
||
| 139 | +179 |
- })+ #' Recursively check if the object contains a named list |
||
| 140 | +180 |
-
+ #' @noRd |
||
| 141 | +181 |
- # manually trigger bookmarking because of the problems reported on windows with bookmarkButton in teal+ #' @keywords internal |
||
| 142 | -77x - | +|||
| 182 | +
- observeEvent(input$do_bookmark, {
+ any_names <- function(x) {
|
|||
| 143 | -! | +|||
| 183 | +103x |
- logger::log_debug("bookmark_manager_srv@1 do_bookmark module clicked.")
+ any( |
||
| 144 | -! | +|||
| 184 | +103x |
- session$doBookmark()+ if (is.list(x)) {
|
||
| 145 | -+ | |||
| 185 | +58x |
- })+ if (!is.null(names(x)) && any(names(x) != "")) TRUE else unlist(lapply(x, any_names)) |
||
| 146 | +186 |
-
+ } else {
|
||
| 147 | -77x - | +187 | +40x |
- invisible(NULL)+ FALSE |
| 148 | +188 |
- })+ } |
||
| 149 | +189 |
- }+ ) |
||
| 150 | +190 |
-
+ } |
| 151 | +1 |
-
+ #' `teal` main module |
||
| 152 | +2 |
- #' @rdname module_bookmark_manager+ #' |
||
| 153 | +3 |
- get_bookmarking_option <- function() {
- |
- ||
| 154 | -77x - | -
- bookmark_option <- getShinyOption("bookmarkStore")
+ #' @description |
||
| 155 | -77x - | +|||
| 4 | +
- if (is.null(bookmark_option) && identical(getOption("shiny.bookmarkStore"), "server")) {
+ #' `r lifecycle::badge("stable")`
|
|||
| 156 | -! | +|||
| 5 | +
- bookmark_option <- getOption("shiny.bookmarkStore")
+ #' Module to create a `teal` app. This module can be called directly instead of [init()] and |
|||
| 157 | +6 |
- }+ #' included in your custom application. Please note that [init()] adds `reporter_previewer_module` |
||
| 158 | -77x - | +|||
| 7 | +
- bookmark_option+ #' automatically, which is not a case when calling `ui/srv_teal` directly. |
|||
| 159 | +8 |
- }+ #' |
||
| 160 | +9 |
-
+ #' @details |
||
| 161 | +10 |
- #' @rdname module_bookmark_manager+ #' |
||
| 162 | +11 |
- need_bookmarking <- function(modules) {
+ #' Module is responsible for creating the main `shiny` app layout and initializing all the necessary |
||
| 163 | -77x - | +|||
| 12 | +
- unlist(rapply2(+ #' components. This module establishes reactive connection between the input `data` and every other |
|||
| 164 | -77x - | +|||
| 13 | +
- modules_bookmarkable(modules),+ #' component in the app. Reactive change of the `data` passed as an argument, reloads the app and |
|||
| 165 | -77x - | +|||
| 14 | +
- Negate(isTRUE)+ #' possibly keeps all input settings the same so the user can continue where one left off. |
|||
| 166 | +15 |
- ))+ #' |
||
| 167 | +16 |
- }+ #' ## data flow in `teal` application |
||
| 168 | +17 |
-
+ #' |
||
| 169 | +18 |
-
+ #' This module supports multiple data inputs but eventually, they are all converted to `reactive` |
||
| 170 | +19 |
- # utilities ----+ #' returning `teal_data` in this module. On this `reactive teal_data` object several actions are |
||
| 171 | +20 |
-
+ #' performed: |
||
| 172 | +21 |
- #' Restore value from bookmark.+ #' - data loading in [`module_init_data`] |
||
| 173 | +22 |
- #'+ #' - data filtering in [`module_filter_data`] |
||
| 174 | +23 |
- #' Get value from bookmark or return default.+ #' - data transformation in [`module_transform_data`] |
||
| 175 | +24 |
#' |
||
| 176 | +25 |
- #' Bookmarks can store not only inputs but also arbitrary values.+ #' ## Fallback on failure |
||
| 177 | +26 |
- #' These values are stored by `onBookmark` callbacks and restored by `onBookmarked` callbacks,+ #' |
||
| 178 | +27 |
- #' and they are placed in the `values` environment in the `session$restoreContext` field.+ #' `teal` is designed in such way that app will never crash if the error is introduced in any |
||
| 179 | +28 |
- #' Using `teal_data_module` makes it impossible to run the callbacks+ #' custom `shiny` module provided by app developer (e.g. [teal_data_module()], [teal_transform_module()]). |
||
| 180 | +29 |
- #' because the app becomes ready before modules execute and callbacks are registered.+ #' If any module returns a failing object, the app will halt the evaluation and display a warning message. |
||
| 181 | +30 |
- #' In those cases the stored values can still be recovered from the `session` object directly.+ #' App user should always have a chance to fix the improper input and continue without restarting the session. |
||
| 182 | +31 |
#' |
||
| 183 | +32 |
- #' Note that variable names in the `values` environment are prefixed with module name space names,+ #' @rdname module_teal |
||
| 184 | +33 |
- #' therefore, when using this function in modules, `value` must be run through the name space function.+ #' @name module_teal |
||
| 185 | +34 |
#' |
||
| 186 | +35 |
- #' @param value (`character(1)`) name of value to restore+ #' @inheritParams module_init_data |
||
| 187 | +36 |
- #' @param default fallback value+ #' @inheritParams init |
||
| 188 | +37 |
#' |
||
| 189 | +38 |
- #' @return+ #' @return `NULL` invisibly |
||
| 190 | +39 |
- #' In an application restored from a server-side bookmark,+ NULL |
||
| 191 | +40 |
- #' the variable specified by `value` from the `values` environment.+ |
||
| 192 | +41 |
- #' Otherwise `default`.+ #' @rdname module_teal |
||
| 193 | +42 |
- #'+ #' @export |
||
| 194 | +43 |
- #' @keywords internal+ ui_teal <- function(id, |
||
| 195 | +44 |
- #'+ modules, |
||
| 196 | +45 |
- restoreValue <- function(value, default) { # nolint: object_name.
- |
- ||
| 197 | -154x - | -
- checkmate::assert_character("value")
- |
- ||
| 198 | -154x - | -
- session_default <- shiny::getDefaultReactiveDomain()+ title = build_app_title(), |
||
| 199 | -154x - | +|||
| 46 | +
- session_parent <- .subset2(session_default, "parent")+ header = tags$p(), |
|||
| 200 | -154x - | +|||
| 47 | +
- session <- if (is.null(session_parent)) session_default else session_parent+ footer = tags$p()) {
|
|||
| 201 | -+ | |||
| 48 | +! |
-
+ checkmate::assert_character(id, max.len = 1, any.missing = FALSE) |
||
| 202 | -154x - | +|||
| 49 | +! |
- if (isTRUE(session$restoreContext$active) && exists(value, session$restoreContext$values, inherits = FALSE)) {
+ checkmate::assert( |
||
| 203 | +50 | ! |
- session$restoreContext$values[[value]]+ .var.name = "title", |
|
| 204 | -+ | |||
| 51 | +! |
- } else {
+ checkmate::check_string(title), |
||
| 205 | -154x - | +|||
| 52 | +! |
- default+ checkmate::check_multi_class(title, c("shiny.tag", "shiny.tag.list", "html"))
|
||
| 206 | +53 |
- }+ ) |
||
| 207 | -+ | |||
| 54 | +! |
- }+ checkmate::assert( |
||
| 208 | -+ | |||
| 55 | +! |
-
+ .var.name = "header", |
||
| 209 | -+ | |||
| 56 | +! |
- #' Compare bookmarks.+ checkmate::check_string(header), |
||
| 210 | -+ | |||
| 57 | +! |
- #'+ checkmate::check_multi_class(header, c("shiny.tag", "shiny.tag.list", "html"))
|
||
| 211 | +58 |
- #' Test if two bookmarks store identical state.+ ) |
||
| 212 | -+ | |||
| 59 | +! |
- #'+ checkmate::assert( |
||
| 213 | -+ | |||
| 60 | +! |
- #' `input` environments are compared one variable at a time and if not identical,+ .var.name = "footer", |
||
| 214 | -+ | |||
| 61 | +! |
- #' values in both bookmarks are reported. States of `datatable`s are stripped+ checkmate::check_string(footer), |
||
| 215 | -+ | |||
| 62 | +! |
- #' of the `time` element before comparing because the time stamp is always different.+ checkmate::check_multi_class(footer, c("shiny.tag", "shiny.tag.list", "html"))
|
||
| 216 | +63 |
- #' The contents themselves are not printed as they are large and the contents are not informative.+ ) |
||
| 217 | +64 |
- #' Elements present in one bookmark and absent in the other are also reported.+ |
||
| 218 | -+ | |||
| 65 | +! |
- #' Differences are printed as messages.+ if (is.character(title)) {
|
||
| 219 | -+ | |||
| 66 | +! |
- #'+ title <- build_app_title(title) |
||
| 220 | +67 |
- #' `values` environments are compared with `all.equal`.+ } else {
|
||
| 221 | -+ | |||
| 68 | +! |
- #'+ validate_app_title_tag(title) |
||
| 222 | +69 |
- #' @section How to use:+ } |
||
| 223 | +70 |
- #' Open an application, change relevant inputs (typically, all of them), and create a bookmark.+ |
||
| 224 | -+ | |||
| 71 | +! |
- #' Then open that bookmark and immediately create a bookmark of that.+ if (checkmate::test_string(header)) {
|
||
| 225 | -+ | |||
| 72 | +! |
- #' If restoring bookmarks occurred properly, the two bookmarks should store the same state.+ header <- tags$p(header) |
||
| 226 | +73 |
- #'+ } |
||
| 227 | +74 |
- #'+ |
||
| 228 | -+ | |||
| 75 | +! |
- #' @param book1,book2 bookmark directories stored in `shiny_bookmarks/`;+ if (checkmate::test_string(footer)) {
|
||
| 229 | -+ | |||
| 76 | +! |
- #' default to the two most recently modified directories+ footer <- tags$p(footer) |
||
| 230 | +77 |
- #'+ } |
||
| 231 | +78 |
- #' @return+ |
||
| 232 | -+ | |||
| 79 | +! |
- #' Invisible `NULL` if bookmarks are identical or if there are no bookmarks to test.+ ns <- NS(id) |
||
| 233 | +80 |
- #' `FALSE` if inconsistencies are detected.+ |
||
| 234 | +81 |
- #'+ # show busy icon when `shiny` session is busy computing stuff |
||
| 235 | +82 |
- #' @keywords internal+ # based on https://stackoverflow.com/questions/17325521/r-shiny-display-loading-message-while-function-is-running/22475216#22475216 # nolint: line_length. |
||
| 236 | -+ | |||
| 83 | +! |
- #'+ shiny_busy_message_panel <- conditionalPanel( |
||
| 237 | -+ | |||
| 84 | +! |
- bookmarks_identical <- function(book1, book2) {
+ condition = "(($('html').hasClass('shiny-busy')) && (document.getElementById('shiny-notification-panel') == null))", # nolint: line_length.
|
||
| 238 | +85 | ! |
- if (!dir.exists("shiny_bookmarks")) {
+ tags$div( |
|
| 239 | +86 | ! |
- message("no bookmark directory")
+ icon("arrows-rotate", class = "fa-spin", prefer_type = "solid"),
|
|
| 240 | +87 | ! |
- return(invisible(NULL))+ "Computing ...", |
|
| 241 | +88 |
- }+ # CSS defined in `custom.css`+ |
+ ||
| 89 | +! | +
+ class = "shinybusymessage" |
||
| 242 | +90 |
-
+ ) |
||
| 243 | -! | +|||
| 91 | +
- ans <- TRUE+ ) |
|||
| 244 | +92 | |||
| 245 | +93 | ! |
- if (missing(book1) && missing(book2)) {
+ fluidPage( |
|
| 246 | +94 | ! |
- dirs <- list.dirs("shiny_bookmarks", recursive = FALSE)
+ id = id, |
|
| 247 | +95 | ! |
- bookmarks_sorted <- basename(rev(dirs[order(file.mtime(dirs))]))+ title = title, |
|
| 248 | +96 | ! |
- if (length(bookmarks_sorted) < 2L) {
+ theme = get_teal_bs_theme(), |
|
| 249 | +97 | ! |
- message("no bookmarks to compare")
+ include_teal_css_js(), |
|
| 250 | +98 | ! |
- return(invisible(NULL))+ tags$header(header), |
|
| 251 | -+ | |||
| 99 | +! |
- }+ tags$hr(class = "my-2"), |
||
| 252 | +100 | ! |
- book1 <- bookmarks_sorted[2L]+ shiny_busy_message_panel, |
|
| 253 | +101 | ! |
- book2 <- bookmarks_sorted[1L]+ tags$div( |
|
| 254 | -+ | |||
| 102 | +! |
- } else {
+ id = ns("tabpanel_wrapper"),
|
||
| 255 | +103 | ! |
- if (!dir.exists(file.path("shiny_bookmarks", book1))) stop(book1, " not found")
+ class = "teal-body", |
|
| 256 | +104 | ! |
- if (!dir.exists(file.path("shiny_bookmarks", book2))) stop(book2, " not found")
+ ui_teal_module(id = ns("teal_modules"), modules = modules)
|
|
| 257 | +105 |
- }+ ), |
||
| 258 | -+ | |||
| 106 | +! |
-
+ tags$div( |
||
| 259 | +107 | ! |
- book1_input <- readRDS(file.path("shiny_bookmarks", book1, "input.rds"))
+ id = ns("options_buttons"),
|
|
| 260 | +108 | ! |
- book2_input <- readRDS(file.path("shiny_bookmarks", book2, "input.rds"))
+ style = "position: absolute; right: 10px;", |
|
| 261 | -+ | |||
| 109 | +! |
-
+ ui_bookmark_panel(ns("bookmark_manager"), modules),
|
||
| 262 | +110 | ! |
- elements_common <- intersect(names(book1_input), names(book2_input))+ tags$button( |
|
| 263 | +111 | ! |
- dt_states <- grepl("_state$", elements_common)
+ class = "btn action-button filter_hamburger", # see sidebar.css for style filter_hamburger |
|
| 264 | +112 | ! |
- if (any(dt_states)) {
+ href = "javascript:void(0)", |
|
| 265 | +113 | ! |
- for (el in elements_common[dt_states]) {
+ onclick = sprintf("toggleFilterPanel('%s');", ns("tabpanel_wrapper")),
|
|
| 266 | +114 | ! |
- book1_input[[el]][["time"]] <- NULL+ title = "Toggle filter panel", |
|
| 267 | +115 | ! |
- book2_input[[el]][["time"]] <- NULL+ icon("fas fa-bars")
|
|
| 268 | +116 |
- }+ ), |
||
| 269 | -+ | |||
| 117 | +! |
- }+ ui_snapshot_manager_panel(ns("snapshot_manager_panel")),
+ |
+ ||
| 118 | +! | +
+ ui_filter_manager_panel(ns("filter_manager_panel"))
|
||
| 270 | +119 |
-
+ ), |
||
| 271 | +120 | ! |
- identicals <- mapply(identical, book1_input[elements_common], book2_input[elements_common])+ tags$script( |
|
| 272 | +121 | ! |
- non_identicals <- names(identicals[!identicals])+ HTML( |
|
| 273 | +122 | ! |
- compares <- sprintf("$ %s:\t%s --- %s", non_identicals, book1_input[non_identicals], book2_input[non_identicals])
+ sprintf( |
|
| 274 | -! | +|||
| 123 | +
- if (length(compares) != 0L) {
+ " |
|||
| 275 | +124 | ! |
- message("common elements not identical: \n", paste(compares, collapse = "\n"))
+ $(document).ready(function() {
|
|
| 276 | +125 | ! |
- ans <- FALSE+ $('#%s').appendTo('#%s');
|
|
| 277 | +126 |
- }+ }); |
||
| 278 | +127 |
-
+ ", |
||
| 279 | +128 | ! |
- elements_boook1 <- setdiff(names(book1_input), names(book2_input))+ ns("options_buttons"),
|
|
| 280 | +129 | ! |
- if (length(elements_boook1) != 0L) {
+ ns("teal_modules-active_tab")
|
|
| 281 | -! | +|||
| 130 | +
- dt_states <- grepl("_state$", elements_boook1)
+ )+ |
+ |||
| 131 | ++ |
+ )+ |
+ ||
| 132 | ++ |
+ ), |
||
| 282 | +133 | ! |
- if (any(dt_states)) {
+ tags$hr(), |
|
| 283 | +134 | ! |
- for (el in elements_boook1[dt_states]) {
+ tags$footer( |
|
| 284 | +135 | ! |
- if (is.list(book1_input[[el]])) book1_input[[el]] <- "--- data table state ---"+ tags$div( |
|
| 285 | -+ | |||
| 136 | +! |
- }+ footer, |
||
| 286 | -+ | |||
| 137 | +! |
- }+ teal.widgets::verbatim_popup_ui(ns("sessionInfo"), "Session Info", type = "link"),
|
||
| 287 | +138 | ! |
- excess1 <- sprintf("$ %s:\t%s", elements_boook1, book1_input[elements_boook1])
+ br(), |
|
| 288 | +139 | ! |
- message("elements only in book1: \n", paste(excess1, collapse = "\n"))
+ ui_teal_lockfile(ns("lockfile")),
|
|
| 289 | +140 | ! |
- ans <- FALSE+ textOutput(ns("identifier"))
|
|
| 290 | +141 |
- }+ ) |
||
| 291 | +142 | ++ |
+ )+ |
+ |
| 143 | ++ |
+ )+ |
+ ||
| 144 | ++ |
+ }+ |
+ ||
| 145 | ||||
| 292 | -! | +|||
| 146 | +
- elements_boook2 <- setdiff(names(book2_input), names(book1_input))+ #' @rdname module_teal |
|||
| 293 | -! | +|||
| 147 | +
- if (length(elements_boook2) != 0L) {
+ #' @export |
|||
| 294 | -! | +|||
| 148 | +
- dt_states <- grepl("_state$", elements_boook1)
+ srv_teal <- function(id, data, modules, filter = teal_slices()) {
|
|||
| 295 | -! | +|||
| 149 | +82x |
- if (any(dt_states)) {
+ checkmate::assert_character(id, max.len = 1, any.missing = FALSE) |
||
| 296 | -! | +|||
| 150 | +82x |
- for (el in elements_boook1[dt_states]) {
+ checkmate::assert_multi_class(data, c("teal_data", "teal_data_module", "reactive"))
|
||
| 297 | -! | +|||
| 151 | +81x |
- if (is.list(book2_input[[el]])) book2_input[[el]] <- "--- data table state ---"+ checkmate::assert_class(modules, "teal_modules")+ |
+ ||
| 152 | +81x | +
+ checkmate::assert_class(filter, "teal_slices") |
||
| 298 | +153 |
- }+ + |
+ ||
| 154 | +81x | +
+ moduleServer(id, function(input, output, session) {
+ |
+ ||
| 155 | +81x | +
+ logger::log_debug("srv_teal initializing.")
|
||
| 299 | +156 |
- }+ |
||
| 300 | -! | +|||
| 157 | +81x |
- excess2 <- sprintf("$ %s:\t%s", elements_boook2, book2_input[elements_boook2])
+ if (getOption("teal.show_js_log", default = FALSE)) {
|
||
| 301 | +158 | ! |
- message("elements only in book2: \n", paste(excess2, collapse = "\n"))
+ shinyjs::showLog() |
|
| 302 | -! | +|||
| 159 | +
- ans <- FALSE+ } |
|||
| 303 | +160 |
- }+ + |
+ ||
| 161 | +81x | +
+ srv_teal_lockfile("lockfile")
|
||
| 304 | +162 | |||
| 305 | -! | +|||
| 163 | +81x |
- book1_values <- readRDS(file.path("shiny_bookmarks", book1, "values.rds"))
+ output$identifier <- renderText( |
||
| 306 | -! | +|||
| 164 | +81x |
- book2_values <- readRDS(file.path("shiny_bookmarks", book2, "values.rds"))
+ paste0("Pid:", Sys.getpid(), " Token:", substr(session$token, 25, 32))
|
||
| 307 | +165 | ++ |
+ )+ |
+ |
| 166 | ||||
| 308 | -! | +|||
| 167 | +81x |
- if (!isTRUE(all.equal(book1_values, book2_values))) {
+ teal.widgets::verbatim_popup_srv( |
||
| 309 | -! | +|||
| 168 | +81x |
- message("different values detected")
+ "sessionInfo", |
||
| 310 | -! | +|||
| 169 | +81x |
- message("choices for numeric filters MAY be different, see RangeFilterState$set_choices")
+ verbatim_content = utils::capture.output(utils::sessionInfo()), |
||
| 311 | -! | +|||
| 170 | +81x |
- ans <- FALSE+ title = "SessionInfo" |
||
| 312 | +171 |
- }+ ) |
||
| 313 | +172 | |||
| 314 | -! | +|||
| 173 | +
- if (ans) message("perfect!")
+ # `JavaScript` code |
|||
| 315 | -! | +|||
| 174 | +81x |
- invisible(NULL)+ run_js_files(files = "init.js") |
||
| 316 | +175 |
- }+ |
||
| 317 | +176 |
-
+ # set timezone in shiny app |
||
| 318 | +177 |
-
+ # timezone is set in the early beginning so it will be available also |
||
| 319 | +178 |
- # Replacement for [base::rapply] which doesn't handle NULL values - skips the evaluation+ # for `DDL` and all shiny modules+ |
+ ||
| 179 | +81x | +
+ get_client_timezone(session$ns)+ |
+ ||
| 180 | +81x | +
+ observeEvent(+ |
+ ||
| 181 | +81x | +
+ eventExpr = input$timezone,+ |
+ ||
| 182 | +81x | +
+ once = TRUE,+ |
+ ||
| 183 | +81x | +
+ handlerExpr = {
+ |
+ ||
| 184 | +! | +
+ session$userData$timezone <- input$timezone+ |
+ ||
| 185 | +! | +
+ logger::log_debug("srv_teal@1 Timezone set to client's timezone: { input$timezone }.")
|
||
| 320 | +186 |
- # of the function and returns NULL for given element.+ } |
||
| 321 | +187 |
- rapply2 <- function(x, f) {
- |
- ||
| 322 | -179x - | -
- if (inherits(x, "list")) {
- |
- ||
| 323 | -77x - | -
- lapply(x, rapply2, f = f)+ ) |
||
| 324 | +188 |
- } else {
+
|
||
| 325 | -102x - | +189 | +81x |
- f(x)+ data_pulled <- srv_init_data("data", data = data)
|
| 326 | -+ | |||
| 190 | +80x |
- }+ data_validated <- srv_validate_reactive_teal_data( |
||
| 327 | -+ | |||
| 191 | +80x |
- }+ "validate", |
| 1 | -+ | |||
| 192 | +80x |
- #' Generate lockfile for application's environment reproducibility+ data = data_pulled, |
||
| 2 | -+ | |||
| 193 | +80x |
- #'+ modules = modules, |
||
| 3 | -+ | |||
| 194 | +80x |
- #' @param lockfile_path (`character`) path to the lockfile.+ validate_shiny_silent_error = FALSE |
||
| 4 | +195 |
- #'+ ) |
||
| 5 | -+ | |||
| 196 | +80x |
- #' @section Different ways of creating lockfile:+ data_rv <- reactive({
|
||
| 6 | -+ | |||
| 197 | +138x |
- #' `teal` leverages [renv::snapshot()], which offers multiple methods for lockfile creation.+ req(inherits(data_validated(), "teal_data")) |
||
| 7 | -+ | |||
| 198 | +68x |
- #'+ is_filter_ok <- check_filter_datanames(filter, ls(teal.code::get_env(data_validated()))) |
||
| 8 | -+ | |||
| 199 | +68x |
- #' - **Working directory lockfile**: `teal`, by default, will create an `implicit` type lockfile that uses+ if (!isTRUE(is_filter_ok)) {
|
||
| 9 | -+ | |||
| 200 | +2x |
- #' `renv::dependencies()` to detect all R packages in the current project's working directory.+ showNotification( |
||
| 10 | -+ | |||
| 201 | +2x |
- #' - **`DESCRIPTION`-based lockfile**: To generate a lockfile based on a `DESCRIPTION` file in your working+ "Some filters were not applied because of incompatibility with data. Contact app developer.", |
||
| 11 | -+ | |||
| 202 | +2x |
- #' directory, set `renv::settings$snapshot.type("explicit")`. The naming convention for `type` follows
+ type = "warning", |
||
| 12 | -+ | |||
| 203 | +2x |
- #' `renv::snapshot()`. For the `"explicit"` type, refer to `renv::settings$package.dependency.fields()` for the+ duration = 10 |
||
| 13 | +204 |
- #' `DESCRIPTION` fields included in the lockfile.+ ) |
||
| 14 | -+ | |||
| 205 | +2x |
- #' - **Custom files-based lockfile**: To specify custom files as the basis for the lockfile, set+ warning(is_filter_ok) |
||
| 15 | +206 |
- #' `renv::settings$snapshot.type("custom")` and configure the `renv.snapshot.filter` option.
+ } |
||
| 16 | -+ | |||
| 207 | +68x |
- #'+ .add_signature_to_data(data_validated()) |
||
| 17 | +208 |
- #' @section lockfile usage:+ }) |
||
| 18 | +209 |
- #' After creating the lockfile, you can restore the application's environment using `renv::restore()`.+ |
||
| 19 | -+ | |||
| 210 | +80x |
- #'+ data_load_status <- reactive({
|
||
| 20 | -+ | |||
| 211 | +73x |
- #' @seealso [renv::snapshot()], [renv::restore()].+ if (inherits(data_pulled(), "teal_data")) {
|
||
| 21 | -+ | |||
| 212 | +68x |
- #'+ "ok" |
||
| 22 | +213 |
- #' @return `NULL`+ # todo: should we hide warnings on top for a data? |
||
| 23 | -+ | |||
| 214 | +5x |
- #'+ } else if (inherits(data, "teal_data_module")) {
|
||
| 24 | -+ | |||
| 215 | +5x |
- #' @name module_teal_lockfile+ "teal_data_module failed" |
||
| 25 | +216 |
- #' @rdname module_teal_lockfile+ } else {
|
||
| 26 | -+ | |||
| 217 | +! |
- #'+ "external failed" |
||
| 27 | +218 |
- #' @keywords internal+ } |
||
| 28 | +219 |
- NULL+ }) |
||
| 29 | +220 | |||
| 30 | -- |
- #' @rdname module_teal_lockfile- |
- ||
| 31 | -+ | |||
| 221 | +80x |
- ui_teal_lockfile <- function(id) {
+ datasets_rv <- if (!isTRUE(attr(filter, "module_specific"))) {
|
||
| 32 | -! | +|||
| 222 | +69x |
- ns <- NS(id)+ eventReactive(data_rv(), {
|
||
| 33 | -! | +|||
| 223 | +59x |
- shiny::tagList(+ req(inherits(data_rv(), "teal_data")) |
||
| 34 | -! | +|||
| 224 | +59x |
- tags$span("", id = ns("lockFileStatus")),
+ logger::log_debug("srv_teal@1 initializing FilteredData")
|
||
| 35 | -! | +|||
| 225 | +59x |
- shinyjs::disabled(downloadLink(ns("lockFileLink"), "Download lockfile"))
+ teal_data_to_filtered_data(data_rv()) |
||
| 36 | +226 |
- )+ }) |
||
| 37 | +227 |
- }+ } |
||
| 38 | +228 | |||
| 39 | -+ | |||
| 229 | +80x |
- #' @rdname module_teal_lockfile+ if (inherits(data, "teal_data_module")) {
|
||
| 40 | -+ | |||
| 230 | +9x |
- srv_teal_lockfile <- function(id) {
+ setBookmarkExclude(c("teal_modules-active_tab"))
|
||
| 41 | -78x - | +231 | +9x |
- moduleServer(id, function(input, output, session) {
+ shiny::insertTab( |
| 42 | -78x - | +232 | +9x |
- logger::log_debug("Initialize srv_teal_lockfile.")
+ inputId = "teal_modules-active_tab", |
| 43 | -78x - | +233 | +9x |
- enable_lockfile_download <- function() {
+ position = "before", |
| 44 | -! | +|||
| 234 | +9x |
- shinyjs::html("lockFileStatus", "Application lockfile ready.")
+ select = TRUE, |
||
| 45 | -! | +|||
| 235 | +9x |
- shinyjs::hide("lockFileStatus", anim = TRUE)
+ tabPanel( |
||
| 46 | -! | +|||
| 236 | +9x |
- shinyjs::enable("lockFileLink")
+ title = icon("fas fa-database"),
|
||
| 47 | -! | +|||
| 237 | +9x |
- output$lockFileLink <- shiny::downloadHandler(+ value = "teal_data_module", |
||
| 48 | -! | +|||
| 238 | +9x |
- filename = function() {
+ tags$div( |
||
| 49 | -! | +|||
| 239 | +9x |
- "renv.lock"+ ui_init_data(session$ns("data")),
|
||
| 50 | -+ | |||
| 240 | +9x |
- },+ ui_validate_reactive_teal_data(session$ns("validate"))
|
||
| 51 | -! | +|||
| 241 | +
- content = function(file) {
+ ) |
|||
| 52 | -! | +|||
| 242 | +
- file.copy(lockfile_path, file)+ ) |
|||
| 53 | -! | +|||
| 243 | +
- file+ ) |
|||
| 54 | +244 |
- },+ |
||
| 55 | -! | +|||
| 245 | +9x |
- contentType = "application/json"+ if (attr(data, "once")) {
|
||
| 56 | -+ | |||
| 246 | +9x |
- )+ observeEvent(data_rv(), once = TRUE, {
|
||
| 57 | -+ | |||
| 247 | +4x |
- }+ logger::log_debug("srv_teal@2 removing data tab.")
|
||
| 58 | -78x - | +|||
| 248 | +
- disable_lockfile_download <- function() {
+ # when once = TRUE we pull data once and then remove data tab |
|||
| 59 | -! | +|||
| 249 | +4x |
- warning("Lockfile creation failed.", call. = FALSE)
+ removeTab("teal_modules-active_tab", target = "teal_data_module")
|
||
| 60 | -! | +|||
| 250 | +
- shinyjs::html("lockFileStatus", "Lockfile creation failed.")
+ }) |
|||
| 61 | -! | +|||
| 251 | +
- shinyjs::hide("lockFileLink")
+ } |
|||
| 62 | +252 |
- }+ } else {
|
||
| 63 | +253 |
-
+ # when no teal_data_module then we want to display messages above tabsetPanel (because there is no data-tab) |
||
| 64 | -78x - | +254 | +71x |
- shiny::onStop(function() {
+ insertUI( |
| 65 | -78x - | +255 | +71x |
- if (file.exists(lockfile_path) && !shiny::isRunning()) {
+ selector = sprintf("#%s", session$ns("tabpanel_wrapper")),
|
| 66 | -1x - | +256 | +71x |
- logger::log_debug("Removing lockfile after shutting down the app")
+ where = "beforeBegin", |
| 67 | -1x - | +257 | +71x |
- file.remove(lockfile_path)+ ui = tags$div(ui_validate_reactive_teal_data(session$ns("validate")), tags$br())
|
| 68 | +258 |
- }+ ) |
||
| 69 | +259 |
- })+ } |
||
| 70 | +260 | |||
| 71 | -78x - | +261 | +80x |
- lockfile_path <- "teal_app.lock"+ module_labels <- unlist(module_labels(modules), use.names = FALSE) |
| 72 | -78x - | +262 | +80x |
- mode <- getOption("teal.lockfile.mode", default = "")
+ slices_global <- methods::new(".slicesGlobal", filter, module_labels)
|
| 73 | -+ | |||
| 263 | +80x |
-
+ modules_output <- srv_teal_module( |
||
| 74 | -78x - | +264 | +80x |
- if (!(mode %in% c("auto", "enabled", "disabled"))) {
+ id = "teal_modules", |
| 75 | -! | +|||
| 265 | +80x |
- stop("'teal.lockfile.mode' option can only be one of \"auto\", \"disabled\" or \"disabled\". ")
+ data_rv = data_rv, |
||
| 76 | -+ | |||
| 266 | +80x |
- }+ datasets = datasets_rv, |
||
| 77 | -+ | |||
| 267 | +80x |
-
+ modules = modules, |
||
| 78 | -78x - | +268 | +80x | +
+ slices_global = slices_global,+ |
+
| 269 | +80x | +
+ data_load_status = data_load_status+ |
+ ||
| 270 | +
- if (mode == "disabled") {
+ ) |
|||
| 79 | -1x - | +271 | +80x |
- logger::log_debug("'teal.lockfile.mode' option is set to 'disabled'. Hiding lockfile download button.")
+ mapping_table <- srv_filter_manager_panel("filter_manager_panel", slices_global = slices_global)
|
| 80 | -1x - | +272 | +80x |
- shinyjs::hide("lockFileLink")
+ snapshots <- srv_snapshot_manager_panel("snapshot_manager_panel", slices_global = slices_global)
|
| 81 | -1x - | +273 | +80x |
- return(NULL)+ srv_bookmark_panel("bookmark_manager", modules)
|
| 82 | +274 |
- }+ }) |
||
| 83 | +275 | |||
| 84 | -77x - | -
- if (file.exists(lockfile_path)) {
- |
- ||
| 85 | -! | -
- logger::log_debug("Lockfile has already been created for this app - skipping automatic creation.")
- |
- ||
| 86 | -! | +276 | +80x |
- enable_lockfile_download()+ invisible(NULL) |
| 87 | -! | +|||
| 277 | +
- return(NULL)+ } |
| 88 | +1 |
- }+ #' Filter state snapshot management |
||
| 89 | +2 |
-
+ #' |
||
| 90 | -77x - | +|||
| 3 | +
- if (mode == "auto" && .is_disabled_lockfile_scenario()) {
+ #' Capture and restore snapshots of the global (app) filter state. |
|||
| 91 | -76x - | +|||
| 4 | +
- logger::log_debug(+ #' |
|||
| 92 | -76x - | +|||
| 5 | +
- "Automatic lockfile creation disabled. Execution scenario satisfies teal:::.is_disabled_lockfile_scenario()."+ #' This module introduces snapshots: stored descriptions of the filter state of the entire application. |
|||
| 93 | +6 |
- )+ #' Snapshots allow the user to save the current filter state of the application for later use in the session, |
||
| 94 | -76x - | +|||
| 7 | +
- shinyjs::hide("lockFileLink")
+ #' as well as to save it to file in order to share it with an app developer or other users, |
|||
| 95 | -76x - | +|||
| 8 | +
- return(NULL)+ #' who in turn can upload it to their own session. |
|||
| 96 | +9 |
- }+ #' |
||
| 97 | +10 |
-
+ #' The snapshot manager is accessed with the camera icon in the tabset bar. |
||
| 98 | -1x - | +|||
| 11 | +
- if (!.is_lockfile_deps_installed()) {
+ #' At the beginning of a session it presents three icons: a camera, an upload, and an circular arrow. |
|||
| 99 | -! | +|||
| 12 | +
- warning("Automatic lockfile creation disabled. `mirai` and `renv` packages must be installed.")
+ #' Clicking the camera captures a snapshot, clicking the upload adds a snapshot from a file |
|||
| 100 | -! | +|||
| 13 | +
- shinyjs::hide("lockFileLink")
+ #' and applies the filter states therein, and clicking the arrow resets initial application state. |
|||
| 101 | -! | +|||
| 14 | +
- return(NULL)+ #' As snapshots are added, they will show up as rows in a table and each will have a select button and a save button. |
|||
| 102 | +15 |
- }+ #' |
||
| 103 | +16 |
-
+ #' @section Server logic: |
||
| 104 | +17 |
- # - Will be run only if the lockfile doesn't exist (see the if-s above)+ #' Snapshots are basically `teal_slices` objects, however, since each module is served by a separate instance |
||
| 105 | +18 |
- # - We render to the tempfile because the process might last after session is closed and we don't+ #' of `FilteredData` and these objects require shared state, `teal_slice` is a `reactiveVal` so `teal_slices` |
||
| 106 | +19 |
- # want to make a "teal_app.renv" then. This is why we copy only during active session.+ #' cannot be stored as is. Therefore, `teal_slices` are reversibly converted to a list of lists representation |
||
| 107 | -1x - | +|||
| 20 | +
- process <- .teal_lockfile_process_invoke(lockfile_path)+ #' (attributes are maintained). |
|||
| 108 | -1x - | +|||
| 21 | +
- observeEvent(process$status(), {
+ #' |
|||
| 109 | -! | +|||
| 22 | +
- if (process$status() %in% c("initial", "running")) {
+ #' Snapshots are stored in a `reactiveVal` as a named list. |
|||
| 110 | -! | +|||
| 23 | +
- shinyjs::html("lockFileStatus", "Creating lockfile...")
+ #' The first snapshot is the initial state of the application and the user can add a snapshot whenever they see fit. |
|||
| 111 | -! | +|||
| 24 | +
- } else if (process$status() == "success") {
+ #' |
|||
| 112 | -! | +|||
| 25 | +
- result <- process$result()+ #' For every snapshot except the initial one, a piece of UI is generated that contains |
|||
| 113 | -! | +|||
| 26 | +
- if (any(grepl("Lockfile written to", result$out))) {
+ #' the snapshot name, a select button to restore that snapshot, and a save button to save it to a file. |
|||
| 114 | -! | +|||
| 27 | +
- logger::log_debug("Lockfile containing { length(result$res$Packages) } packages created.")
+ #' The initial snapshot is restored by a separate "reset" button. |
|||
| 115 | -! | +|||
| 28 | +
- if (any(grepl("(WARNING|ERROR):", result$out))) {
+ #' It cannot be saved directly but a user is welcome to capture the initial state as a snapshot and save that. |
|||
| 116 | -! | +|||
| 29 | +
- warning("Lockfile created with warning(s) or error(s):", call. = FALSE)
+ #' |
|||
| 117 | -! | +|||
| 30 | +
- for (i in result$out) {
+ #' @section Snapshot mechanics: |
|||
| 118 | -! | +|||
| 31 | +
- warning(i, call. = FALSE)+ #' When a snapshot is captured, the user is prompted to name it. |
|||
| 119 | +32 |
- }+ #' Names are displayed as is but since they are used to create button ids, |
||
| 120 | +33 |
- }+ #' under the hood they are converted to syntactically valid strings. |
||
| 121 | -! | +|||
| 34 | +
- enable_lockfile_download()+ #' New snapshot names are validated so that their valid versions are unique. |
|||
| 122 | +35 |
- } else {
+ #' Leading and trailing white space is trimmed. |
||
| 123 | -! | +|||
| 36 | +
- disable_lockfile_download()+ #' |
|||
| 124 | +37 |
- }+ #' The module can read the global state of the application from `slices_global` and `mapping_matrix`. |
||
| 125 | -! | +|||
| 38 | +
- } else if (process$status() == "error") {
+ #' The former provides a list of all existing `teal_slice`s and the latter says which slice is active in which module. |
|||
| 126 | -! | +|||
| 39 | +
- disable_lockfile_download()+ #' Once a name has been accepted, `slices_global` is converted to a list of lists - a snapshot. |
|||
| 127 | +40 |
- }+ #' The snapshot contains the `mapping` attribute of the initial application state |
||
| 128 | +41 |
- })+ #' (or one that has been restored), which may not reflect the current one, |
||
| 129 | +42 |
-
+ #' so `mapping_matrix` is transformed to obtain the current mapping, i.e. a list that, |
||
| 130 | -1x - | +|||
| 43 | +
- NULL+ #' when passed to the `mapping` argument of [teal_slices()], would result in the current mapping. |
|||
| 131 | +44 |
- })+ #' This is substituted as the snapshot's `mapping` attribute and the snapshot is added to the snapshot list. |
||
| 132 | +45 |
- }+ #' |
||
| 133 | +46 |
-
+ #' To restore app state, a snapshot is retrieved from storage and rebuilt into a `teal_slices` object. |
||
| 134 | +47 |
- utils::globalVariables(c("opts", "sysenv", "libpaths", "wd", "lockfilepath", "run")) # needed for mirai call
+ #' Then state of all `FilteredData` objects (provided in `datasets`) is cleared |
||
| 135 | +48 |
- #' @rdname module_teal_lockfile+ #' and set anew according to the `mapping` attribute of the snapshot. |
||
| 136 | +49 |
- .teal_lockfile_process_invoke <- function(lockfile_path) {
+ #' The snapshot is then set as the current content of `slices_global`. |
||
| 137 | -1x - | +|||
| 50 | +
- mirai_obj <- NULL+ #' |
|||
| 138 | -1x - | +|||
| 51 | +
- process <- shiny::ExtendedTask$new(function() {
+ #' To save a snapshot, the snapshot is retrieved and reassembled just like for restoring, |
|||
| 139 | -1x - | +|||
| 52 | +
- m <- mirai::mirai(+ #' and then saved to file with [slices_store()]. |
|||
| 140 | +53 |
- {
+ #' |
||
| 141 | -1x - | +|||
| 54 | +
- options(opts)+ #' When a snapshot is uploaded, it will first be added to storage just like a newly created one, |
|||
| 142 | -1x - | +|||
| 55 | +
- do.call(Sys.setenv, sysenv)+ #' and then used to restore app state much like a snapshot taken from storage. |
|||
| 143 | -1x - | +|||
| 56 | +
- .libPaths(libpaths)+ #' Upon clicking the upload icon the user will be prompted for a file to upload |
|||
| 144 | -1x - | +|||
| 57 | +
- setwd(wd)+ #' and may choose to name the new snapshot. The name defaults to the name of the file (the extension is dropped) |
|||
| 145 | -1x - | +|||
| 58 | +
- run(lockfile_path = lockfile_path)+ #' and normal naming rules apply. Loading the file yields a `teal_slices` object, |
|||
| 146 | +59 |
- },+ #' which is disassembled for storage and used directly for restoring app state. |
||
| 147 | -1x - | +|||
| 60 | +
- run = .renv_snapshot,+ #' |
|||
| 148 | -1x - | +|||
| 61 | +
- lockfile_path = lockfile_path,+ #' @section Transferring snapshots: |
|||
| 149 | -1x - | +|||
| 62 | +
- opts = options(),+ #' Snapshots uploaded from disk should only be used in the same application they come from, |
|||
| 150 | -1x - | +|||
| 63 | +
- libpaths = .libPaths(),+ #' _i.e._ an application that uses the same data and the same modules. |
|||
| 151 | -1x - | +|||
| 64 | +
- sysenv = as.list(Sys.getenv()),+ #' To ensure this is the case, `init` stamps `teal_slices` with an app id that is stored in the `app_id` attribute of |
|||
| 152 | -1x - | +|||
| 65 | +
- wd = getwd()+ #' a `teal_slices` object. When a snapshot is restored from file, its `app_id` is compared to that |
|||
| 153 | +66 |
- )+ #' of the current app state and only if the match is the snapshot admitted to the session. |
||
| 154 | -1x - | +|||
| 67 | +
- mirai_obj <<- m+ #' |
|||
| 155 | -1x - | +|||
| 68 | +
- m+ #' @section Bookmarks: |
|||
| 156 | +69 |
- })+ #' An `onBookmark` callback creates a snapshot of the current filter state. |
||
| 157 | +70 |
-
+ #' This is done on the app session, not the module session. |
||
| 158 | -1x - | +|||
| 71 | +
- shiny::onStop(function() {
+ #' (The snapshot will be retrieved by `module_teal` in order to set initial app state in a restored app.) |
|||
| 159 | -1x - | +|||
| 72 | +
- if (mirai::unresolved(mirai_obj)) {
+ #' Then that snapshot, and the previous snapshot history are dumped into the `values.rds` file in `<bookmark_dir>`. |
|||
| 160 | -! | +|||
| 73 | +
- logger::log_debug("Terminating a running lockfile process...")
+ #' |
|||
| 161 | -! | +|||
| 74 | +
- mirai::stop_mirai(mirai_obj) # this doesn't stop running - renv will be created even if session is closed+ #' @param id (`character(1)`) `shiny` module instance id. |
|||
| 162 | +75 |
- }+ #' @param slices_global (`reactiveVal`) that contains a `teal_slices` object |
||
| 163 | +76 |
- })+ #' containing all `teal_slice`s existing in the app, both active and inactive. |
||
| 164 | +77 |
-
+ #' |
||
| 165 | -1x - | +|||
| 78 | +
- suppressWarnings({ # 'package:stats' may not be available when loading
+ #' @return `list` containing the snapshot history, where each element is an unlisted `teal_slices` object. |
|||
| 166 | -1x - | +|||
| 79 | +
- process$invoke()+ #' |
|||
| 167 | +80 |
- })+ #' @name module_snapshot_manager |
||
| 168 | +81 |
-
+ #' @rdname module_snapshot_manager |
||
| 169 | -1x - | +|||
| 82 | +
- logger::log_debug("Lockfile creation started based on { getwd() }.")
+ #' |
|||
| 170 | +83 |
-
+ #' @author Aleksander Chlebowski |
||
| 171 | -1x - | +|||
| 84 | +
- process+ #' @keywords internal |
|||
| 172 | +85 |
- }+ NULL |
||
| 173 | +86 | |||
| 174 | +87 |
- #' @rdname module_teal_lockfile+ #' @rdname module_snapshot_manager |
||
| 175 | +88 |
- .renv_snapshot <- function(lockfile_path) {
- |
- ||
| 176 | -1x - | -
- out <- utils::capture.output(+ ui_snapshot_manager_panel <- function(id) {
|
||
| 177 | -1x - | +|||
| 89 | +! |
- res <- renv::snapshot(+ ns <- NS(id) |
||
| 178 | -1x - | +|||
| 90 | +! |
- lockfile = lockfile_path,+ tags$button( |
||
| 179 | -1x - | +|||
| 91 | +! |
- prompt = FALSE,+ id = ns("show_snapshot_manager"),
|
||
| 180 | -1x - | +|||
| 92 | +! |
- force = TRUE,+ class = "btn action-button wunder_bar_button", |
||
| 181 | -1x - | +|||
| 93 | +! |
- type = renv::settings$snapshot.type() # see the section "Different ways of creating lockfile" above here+ title = "View filter mapping", |
||
| 182 | -+ | |||
| 94 | +! |
- )+ suppressMessages(icon("fas fa-camera"))
|
||
| 183 | +95 |
) |
||
| 184 | -- | - - | -||
| 185 | -1x - | -
- list(out = out, res = res)- |
- ||
| 186 | +96 |
} |
||
| 187 | +97 | |||
| 188 | +98 |
- #' @rdname module_teal_lockfile+ #' @rdname module_snapshot_manager |
||
| 189 | +99 |
- .is_lockfile_deps_installed <- function() {
+ srv_snapshot_manager_panel <- function(id, slices_global) {
|
||
| 190 | -1x - | +100 | +80x |
- requireNamespace("mirai", quietly = TRUE) && requireNamespace("renv", quietly = TRUE)
+ moduleServer(id, function(input, output, session) {
|
| 191 | -+ | |||
| 101 | +80x |
- }+ logger::log_debug("srv_snapshot_manager_panel initializing")
|
||
| 192 | -+ | |||
| 102 | +80x |
-
+ setBookmarkExclude(c("show_snapshot_manager"))
|
||
| 193 | -+ | |||
| 103 | +80x |
- #' @rdname module_teal_lockfile+ observeEvent(input$show_snapshot_manager, {
|
||
| 194 | -+ | |||
| 104 | +! |
- .is_disabled_lockfile_scenario <- function() {
+ logger::log_debug("srv_snapshot_manager_panel@1 show_snapshot_manager button has been clicked.")
|
||
| 195 | -76x - | +|||
| 105 | +! |
- identical(Sys.getenv("CALLR_IS_RUNNING"), "true") || # inside callr process
+ showModal( |
||
| 196 | -76x - | +|||
| 106 | +! |
- identical(Sys.getenv("TESTTHAT"), "true") || # inside devtools::test
+ modalDialog( |
||
| 197 | -76x - | +|||
| 107 | +! |
- !identical(Sys.getenv("QUARTO_PROJECT_ROOT"), "") || # inside Quarto process
+ ui_snapshot_manager(session$ns("module")),
|
||
| 198 | -+ | |||
| 108 | +! |
- (+ class = "snapshot_manager_modal", |
||
| 199 | -76x - | +|||
| 109 | +! |
- ("CheckExEnv" %in% search()) || any(c("_R_CHECK_TIMINGS_", "_R_CHECK_LICENSE_") %in% names(Sys.getenv()))
+ size = "m", |
||
| 200 | -76x - | +|||
| 110 | +! |
- ) # inside R CMD CHECK+ footer = NULL, |
||
| 201 | -+ | |||
| 111 | +! |
- }+ easyClose = TRUE |
| 1 | +112 |
- #' Execute and validate `teal_data_module`+ ) |
||
| 2 | +113 |
- #'+ ) |
||
| 3 | +114 |
- #' This is a low level module to handle `teal_data_module` execution and validation.+ }) |
||
| 4 | -+ | |||
| 115 | +80x |
- #' [teal_transform_module()] inherits from [teal_data_module()] so it is handled by this module too.+ srv_snapshot_manager("module", slices_global = slices_global)
|
||
| 5 | +116 |
- #' [srv_teal()] accepts various `data` objects and eventually they are all transformed to `reactive`+ }) |
||
| 6 | +117 |
- #' [teal_data()] which is a standard data class in whole `teal` framework.+ } |
||
| 7 | +118 |
- #'+ |
||
| 8 | +119 |
- #' @section data validation:+ #' @rdname module_snapshot_manager |
||
| 9 | +120 |
- #'+ ui_snapshot_manager <- function(id) {
|
||
| 10 | -+ | |||
| 121 | +! |
- #' Executed [teal_data_module()] is validated and output is validated for consistency.+ ns <- NS(id) |
||
| 11 | -+ | |||
| 122 | +! |
- #' Output `data` is invalid if:+ tags$div( |
||
| 12 | -+ | |||
| 123 | +! |
- #' 1. [teal_data_module()] is invalid if server doesn't return `reactive`. **Immediately crashes an app!**+ class = "manager_content", |
||
| 13 | -+ | |||
| 124 | +! |
- #' 2. `reactive` throws a `shiny.error` - happens when module creating [teal_data()] fails.+ tags$div( |
||
| 14 | -+ | |||
| 125 | +! |
- #' 3. `reactive` returns `qenv.error` - happens when [teal_data()] evaluates a failing code.+ class = "manager_table_row", |
||
| 15 | -+ | |||
| 126 | +! |
- #' 4. `reactive` object doesn't return [teal_data()].+ tags$span(tags$b("Snapshot manager")),
|
||
| 16 | -+ | |||
| 127 | +! |
- #' 5. [teal_data()] object lacks any `datanames` specified in the `modules` argument.+ actionLink(ns("snapshot_add"), label = NULL, icon = icon("fas fa-camera"), title = "add snapshot"),
|
||
| 17 | -+ | |||
| 128 | +! |
- #'+ actionLink(ns("snapshot_load"), label = NULL, icon = icon("fas fa-upload"), title = "upload snapshot"),
|
||
| 18 | -+ | |||
| 129 | +! |
- #' `teal` (observers in `srv_teal`) always waits to render an app until `reactive` `teal_data` is+ actionLink(ns("snapshot_reset"), label = NULL, icon = icon("fas fa-undo"), title = "reset initial state"),
|
||
| 19 | -+ | |||
| 130 | +! |
- #' returned. If error 2-4 occurs, relevant error message is displayed to the app user. Once the issue is+ NULL |
||
| 20 | +131 |
- #' resolved, the app will continue to run. `teal` guarantees that errors in data don't crash the app+ ), |
||
| 21 | -+ | |||
| 132 | +! |
- #' (except error 1).+ uiOutput(ns("snapshot_list"))
|
||
| 22 | +133 |
- #'+ ) |
||
| 23 | +134 |
- #' @param id (`character(1)`) Module id+ } |
||
| 24 | +135 |
- #' @param data (`reactive teal_data`)+ |
||
| 25 | +136 |
- #' @param data_module (`teal_data_module`)+ #' @rdname module_snapshot_manager |
||
| 26 | +137 |
- #' @param modules (`teal_modules` or `teal_module`) For `datanames` validation purpose+ srv_snapshot_manager <- function(id, slices_global) {
|
||
| 27 | -+ | |||
| 138 | +80x |
- #' @param validate_shiny_silent_error (`logical`) If `TRUE`, then `shiny.silent.error` is validated and+ checkmate::assert_character(id) |
||
| 28 | +139 |
- #' @param is_transformer_failed (`reactiveValues`) contains `logical` flags named after each transformer.+ |
||
| 29 | -+ | |||
| 140 | +80x |
- #' Help to determine if any previous transformer failed, so that following transformers can be disabled+ moduleServer(id, function(input, output, session) {
|
||
| 30 | -+ | |||
| 141 | +80x |
- #' and display a generic failure message.+ logger::log_debug("srv_snapshot_manager initializing")
|
||
| 31 | +142 |
- #'+ |
||
| 32 | +143 |
- #' @return `reactive` `teal_data`+ # Set up bookmarking callbacks ---- |
||
| 33 | +144 |
- #'+ # Register bookmark exclusions (all buttons and text fields). |
||
| 34 | -+ | |||
| 145 | +80x |
- #' @rdname module_teal_data+ setBookmarkExclude(c( |
||
| 35 | -+ | |||
| 146 | +80x |
- #' @name module_teal_data+ "snapshot_add", "snapshot_load", "snapshot_reset", |
||
| 36 | -+ | |||
| 147 | +80x |
- #' @keywords internal+ "snapshot_name_accept", "snaphot_file_accept", |
||
| 37 | -+ | |||
| 148 | +80x |
- NULL+ "snapshot_name", "snapshot_file" |
||
| 38 | +149 |
-
+ )) |
||
| 39 | +150 |
- #' @rdname module_teal_data+ # Add snapshot history to bookmark. |
||
| 40 | -+ | |||
| 151 | +80x |
- ui_teal_data <- function(id, data_module = function(id) NULL) {
+ session$onBookmark(function(state) {
|
||
| 41 | +152 | ! |
- checkmate::assert_string(id)+ logger::log_debug("srv_snapshot_manager@onBookmark: storing snapshot and bookmark history")
|
|
| 42 | +153 | ! |
- checkmate::assert_function(data_module, args = "id")+ state$values$snapshot_history <- snapshot_history() # isolate this? |
|
| 43 | -! | +|||
| 154 | +
- ns <- NS(id)+ }) |
|||
| 44 | +155 | |||
| 45 | -! | +|||
| 156 | +80x |
- shiny::tagList(+ ns <- session$ns |
||
| 46 | -! | +|||
| 157 | +
- tags$div(id = ns("wrapper"), data_module(id = ns("data"))),
+
|
|||
| 47 | -! | +|||
| 158 | +
- ui_validate_reactive_teal_data(ns("validate"))
+ # Track global filter states ---- |
|||
| 48 | -+ | |||
| 159 | +80x |
- )+ snapshot_history <- reactiveVal({
|
||
| 49 | +160 |
- }+ # Restore directly from bookmarked state, if applicable.+ |
+ ||
| 161 | +80x | +
+ restoreValue( |
||
| 50 | -+ | |||
| 162 | +80x |
-
+ ns("snapshot_history"),
|
||
| 51 | -+ | |||
| 163 | +80x |
- #' @rdname module_teal_data+ list("Initial application state" = shiny::isolate(as.list(slices_global$all_slices(), recursive = TRUE)))
|
||
| 52 | +164 |
- srv_teal_data <- function(id,+ ) |
||
| 53 | +165 |
- data_module = function(id) NULL,+ }) |
||
| 54 | +166 |
- modules = NULL,+ |
||
| 55 | +167 |
- validate_shiny_silent_error = TRUE,+ # Snapshot current application state ---- |
||
| 56 | +168 |
- is_transformer_failed = reactiveValues()) {
+ # Name snaphsot. |
||
| 57 | -19x - | +169 | +80x |
- checkmate::assert_string(id)+ observeEvent(input$snapshot_add, {
|
| 58 | -19x - | +|||
| 170 | +! |
- checkmate::assert_function(data_module, args = "id")+ logger::log_debug("srv_snapshot_manager: snapshot_add button clicked")
|
||
| 59 | -19x - | +|||
| 171 | +! |
- checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"), null.ok = TRUE)
+ showModal( |
||
| 60 | -19x - | +|||
| 172 | +! |
- checkmate::assert_class(is_transformer_failed, "reactivevalues")+ modalDialog( |
||
| 61 | -+ | |||
| 173 | +! |
-
+ textInput(ns("snapshot_name"), "Name the snapshot", width = "100%", placeholder = "Meaningful, unique name"),
|
||
| 62 | -19x - | +|||
| 174 | +! |
- moduleServer(id, function(input, output, session) {
+ footer = tagList( |
||
| 63 | -19x - | +|||
| 175 | +! |
- logger::log_debug("srv_teal_data initializing.")
+ actionButton(ns("snapshot_name_accept"), "Accept", icon = icon("far fa-thumbs-up")),
|
||
| 64 | -19x - | +|||
| 176 | +! |
- is_transformer_failed[[id]] <- FALSE+ modalButton(label = "Cancel", icon = icon("far fa-thumbs-down"))
|
||
| 65 | -19x - | +|||
| 177 | +
- data_out <- data_module(id = "data")+ ), |
|||
| 66 | -19x - | +|||
| 178 | +! |
- data_handled <- reactive(tryCatch(data_out(), error = function(e) e))+ size = "s" |
||
| 67 | -19x - | +|||
| 179 | +
- observeEvent(data_handled(), {
+ ) |
|||
| 68 | -21x - | +|||
| 180 | +
- if (!inherits(data_handled(), "teal_data")) {
+ ) |
|||
| 69 | -6x - | +|||
| 181 | +
- is_transformer_failed[[id]] <- TRUE+ }) |
|||
| 70 | +182 |
- } else {
+ # Store snaphsot. |
||
| 71 | -15x - | -
- is_transformer_failed[[id]] <- FALSE- |
- ||
| 72 | -+ | 183 | +80x |
- }+ observeEvent(input$snapshot_name_accept, {
|
| 73 | -+ | |||
| 184 | +! |
- })+ logger::log_debug("srv_snapshot_manager: snapshot_name_accept button clicked")
|
||
| 74 | -+ | |||
| 185 | +! |
-
+ snapshot_name <- trimws(input$snapshot_name) |
||
| 75 | -19x - | +|||
| 186 | +! |
- is_previous_failed <- reactive({
+ if (identical(snapshot_name, "")) {
|
||
| 76 | -19x - | +|||
| 187 | +! |
- idx_this <- which(names(is_transformer_failed) == id)+ logger::log_debug("srv_snapshot_manager: snapshot name rejected")
|
||
| 77 | -19x - | +|||
| 188 | +! |
- is_transformer_failed_list <- reactiveValuesToList(is_transformer_failed)+ showNotification( |
||
| 78 | -19x - | +|||
| 189 | +! |
- idx_failures <- which(unlist(is_transformer_failed_list))+ "Please name the snapshot.", |
||
| 79 | -19x - | +|||
| 190 | +! |
- any(idx_failures < idx_this)+ type = "message" |
||
| 80 | +191 |
- })+ ) |
||
| 81 | -+ | |||
| 192 | +! |
-
+ updateTextInput(inputId = "snapshot_name", value = "", placeholder = "Meaningful, unique name") |
||
| 82 | -19x - | +|||
| 193 | +! |
- observeEvent(is_previous_failed(), {
+ } else if (is.element(make.names(snapshot_name), make.names(names(snapshot_history())))) {
|
||
| 83 | -19x - | +|||
| 194 | +! |
- if (is_previous_failed()) {
+ logger::log_debug("srv_snapshot_manager: snapshot name rejected")
|
||
| 84 | +195 | ! |
- shinyjs::disable("wrapper")
+ showNotification( |
|
| 85 | -+ | |||
| 196 | +! |
- } else {
+ "This name is in conflict with other snapshot names. Please choose a different one.", |
||
| 86 | -19x - | +|||
| 197 | +! |
- shinyjs::enable("wrapper")
+ type = "message" |
||
| 87 | +198 |
- }+ ) |
||
| 88 | -+ | |||
| 199 | +! |
- })+ updateTextInput(inputId = "snapshot_name", value = "", placeholder = "Meaningful, unique name") |
||
| 89 | +200 |
-
+ } else {
|
||
| 90 | -19x - | +|||
| 201 | +! |
- srv_validate_reactive_teal_data(+ logger::log_debug("srv_snapshot_manager: snapshot name accepted, adding snapshot")
|
||
| 91 | -19x - | +|||
| 202 | +! |
- "validate",+ snapshot <- as.list(slices_global$all_slices(), recursive = TRUE) |
||
| 92 | -19x - | +|||
| 203 | +! |
- data = data_handled,+ snapshot_update <- c(snapshot_history(), list(snapshot)) |
||
| 93 | -19x - | +|||
| 204 | +! |
- modules = modules,+ names(snapshot_update)[length(snapshot_update)] <- snapshot_name |
||
| 94 | -19x - | +|||
| 205 | +! |
- validate_shiny_silent_error = validate_shiny_silent_error,+ snapshot_history(snapshot_update) |
||
| 95 | -19x - | +|||
| 206 | +! |
- hide_validation_error = is_previous_failed+ removeModal() |
||
| 96 | +207 |
- )+ # Reopen filter manager modal by clicking button in the main application. |
||
| 97 | -+ | |||
| 208 | +! |
- })+ shinyjs::click(id = "teal-wunder_bar-show_snapshot_manager", asis = TRUE) |
||
| 98 | +209 |
- }+ } |
||
| 99 | +210 |
-
+ }) |
||
| 100 | +211 |
- #' @rdname module_teal_data+ |
||
| 101 | +212 |
- ui_validate_reactive_teal_data <- function(id) {
- |
- ||
| 102 | -77x - | -
- ns <- NS(id)+ # Upload a snapshot file ---- |
||
| 103 | -77x - | +|||
| 213 | +
- tagList(+ # Select file. |
|||
| 104 | -77x - | +214 | +80x |
- div(+ observeEvent(input$snapshot_load, {
|
| 105 | -77x - | +|||
| 215 | +! |
- id = ns("validate_messages"),
+ logger::log_debug("srv_snapshot_manager: snapshot_load button clicked")
|
||
| 106 | -77x - | +|||
| 216 | +! |
- class = "teal_validated",+ showModal( |
||
| 107 | -77x - | +|||
| 217 | +! |
- ui_validate_error(ns("silent_error")),
+ modalDialog( |
||
| 108 | -77x - | +|||
| 218 | +! |
- ui_check_class_teal_data(ns("class_teal_data")),
+ fileInput(ns("snapshot_file"), "Choose snapshot file", accept = ".json", width = "100%"),
|
||
| 109 | -77x - | +|||
| 219 | +! |
- ui_check_shiny_warnings(ns("shiny_warnings"))
+ textInput( |
||
| 110 | -+ | |||
| 220 | +! |
- ),+ ns("snapshot_name"),
|
||
| 111 | -77x - | +|||
| 221 | +! |
- div(+ "Name the snapshot (optional)", |
||
| 112 | -77x - | +|||
| 222 | +! |
- class = "teal_validated",+ width = "100%", |
||
| 113 | -77x - | +|||
| 223 | +! |
- uiOutput(ns("previous_failed"))
+ placeholder = "Meaningful, unique name" |
||
| 114 | +224 |
- )+ ), |
||
| 115 | -+ | |||
| 225 | +! |
- )+ footer = tagList( |
||
| 116 | -+ | |||
| 226 | +! |
- }+ actionButton(ns("snaphot_file_accept"), "Accept", icon = icon("far fa-thumbs-up")),
|
||
| 117 | -+ | |||
| 227 | +! |
-
+ modalButton(label = "Cancel", icon = icon("far fa-thumbs-down"))
|
||
| 118 | +228 |
- #' @rdname module_teal_data+ ) |
||
| 119 | +229 |
- srv_validate_reactive_teal_data <- function(id, # nolint: object_length+ ) |
||
| 120 | +230 |
- data,+ ) |
||
| 121 | +231 |
- modules = NULL,+ }) |
||
| 122 | +232 |
- validate_shiny_silent_error = FALSE,+ # Store new snapshot to list and restore filter states. |
||
| 123 | -+ | |||
| 233 | +80x |
- hide_validation_error = reactive(FALSE)) {
+ observeEvent(input$snaphot_file_accept, {
|
||
| 124 | -172x - | +|||
| 234 | +! |
- checkmate::assert_string(id)+ logger::log_debug("srv_snapshot_manager: snapshot_file_accept button clicked")
|
||
| 125 | -172x - | +|||
| 235 | +! |
- checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"), null.ok = TRUE)
+ snapshot_name <- trimws(input$snapshot_name) |
||
| 126 | -172x - | +|||
| 236 | +! |
- checkmate::assert_flag(validate_shiny_silent_error)+ if (identical(snapshot_name, "")) {
|
||
| 127 | -+ | |||
| 237 | +! |
-
+ logger::log_debug("srv_snapshot_manager: no snapshot name provided, naming after file")
|
||
| 128 | -172x - | +|||
| 238 | +! |
- moduleServer(id, function(input, output, session) {
+ snapshot_name <- tools::file_path_sans_ext(input$snapshot_file$name) |
||
| 129 | +239 |
- # there is an empty reactive cycle on `init` and `data_rv` has `shiny.silent.error` class- |
- ||
| 130 | -172x - | -
- srv_validate_error("silent_error", data, validate_shiny_silent_error)
+ } |
||
| 131 | -172x - | +|||
| 240 | +! |
- srv_check_class_teal_data("class_teal_data", data)
+ if (is.element(make.names(snapshot_name), make.names(names(snapshot_history())))) {
|
||
| 132 | -172x - | +|||
| 241 | +! |
- srv_check_shiny_warnings("shiny_warnings", data, modules)
+ logger::log_debug("srv_snapshot_manager: snapshot name rejected")
|
||
| 133 | -172x - | +|||
| 242 | +! |
- output$previous_failed <- renderUI({
+ showNotification( |
||
| 134 | -162x - | +|||
| 243 | +! |
- if (hide_validation_error()) {
+ "This name is in conflict with other snapshot names. Please choose a different one.", |
||
| 135 | +244 | ! |
- shinyjs::hide("validate_messages")
+ type = "message"+ |
+ |
| 245 | ++ |
+ ) |
||
| 136 | +246 | ! |
- tags$div("One of previous transformers failed. Please fix and continue.", class = "teal-output-warning")
+ updateTextInput(inputId = "snapshot_name", value = "", placeholder = "Meaningful, unique name") |
|
| 137 | +247 |
} else {
|
||
| 138 | -162x - | +|||
| 248 | +
- shinyjs::show("validate_messages")
+ # Restore snapshot and verify app compatibility. |
|||
| 139 | -162x - | +|||
| 249 | +! |
- NULL+ logger::log_debug("srv_snapshot_manager: snapshot name accepted, loading snapshot")
|
||
| 140 | -+ | |||
| 250 | +! |
- }+ snapshot_state <- try(slices_restore(input$snapshot_file$datapath)) |
||
| 141 | -+ | |||
| 251 | +! |
- })+ if (!inherits(snapshot_state, "modules_teal_slices")) {
|
||
| 142 | -+ | |||
| 252 | +! |
-
+ logger::log_debug("srv_snapshot_manager: snapshot file corrupt")
|
||
| 143 | -172x - | +|||
| 253 | +! |
- .trigger_on_success(data)+ showNotification( |
||
| 144 | -+ | |||
| 254 | +! |
- })+ "File appears to be corrupt.", |
||
| 145 | -+ | |||
| 255 | +! |
- }+ type = "error" |
||
| 146 | +256 |
-
+ ) |
||
| 147 | -+ | |||
| 257 | +! |
- #' @keywords internal+ } else if (!identical(attr(snapshot_state, "app_id"), attr(slices_global$all_slices(), "app_id"))) {
|
||
| 148 | -+ | |||
| 258 | +! |
- ui_validate_error <- function(id) {
+ logger::log_debug("srv_snapshot_manager: snapshot not compatible with app")
|
||
| 149 | -77x - | +|||
| 259 | +! |
- ns <- NS(id)+ showNotification( |
||
| 150 | -77x - | +|||
| 260 | +! |
- uiOutput(ns("message"))
+ "This snapshot file is not compatible with the app and cannot be loaded.", |
||
| 151 | -+ | |||
| 261 | +! |
- }+ type = "warning" |
||
| 152 | +262 |
-
+ ) |
||
| 153 | +263 |
- #' @keywords internal+ } else {
|
||
| 154 | +264 |
- srv_validate_error <- function(id, data, validate_shiny_silent_error) {
- |
- ||
| 155 | -172x - | -
- checkmate::assert_string(id)+ # Add to snapshot history. |
||
| 156 | -172x - | +|||
| 265 | +! |
- checkmate::assert_flag(validate_shiny_silent_error)+ logger::log_debug("srv_snapshot_manager: snapshot loaded, adding to history")
|
||
| 157 | -172x - | +|||
| 266 | +! |
- moduleServer(id, function(input, output, session) {
+ snapshot <- as.list(slices_global$all_slices(), recursive = TRUE) |
||
| 158 | -172x - | +|||
| 267 | +! |
- output$message <- renderUI({
+ snapshot_update <- c(snapshot_history(), list(snapshot)) |
||
| 159 | -175x - | +|||
| 268 | +! |
- is_shiny_silent_error <- inherits(data(), "shiny.silent.error") && identical(data()$message, "")+ names(snapshot_update)[length(snapshot_update)] <- snapshot_name |
||
| 160 | -169x - | +|||
| 269 | +! |
- if (inherits(data(), "qenv.error")) {
+ snapshot_history(snapshot_update) |
||
| 161 | -2x - | +|||
| 270 | +
- validate(+ ### Begin simplified restore procedure. ### |
|||
| 162 | -2x - | +|||
| 271 | +! |
- need(+ logger::log_debug("srv_snapshot_manager: restoring snapshot")
|
||
| 163 | -2x - | +|||
| 272 | +! |
- FALSE,+ slices_global$slices_set(snapshot_state) |
||
| 164 | -2x - | +|||
| 273 | +! |
- paste(+ removeModal() |
||
| 165 | -2x - | +|||
| 274 | +
- "Error when executing the `data` module:",+ ### End simplified restore procedure. ### |
|||
| 166 | -2x - | +|||
| 275 | +
- strip_style(paste(data()$message, collapse = "\n")),+ } |
|||
| 167 | -2x - | +|||
| 276 | +
- "\nCheck your inputs or contact app developer if error persists.",+ } |
|||
| 168 | -2x - | +|||
| 277 | +
- collapse = "\n"+ }) |
|||
| 169 | +278 |
- )+ # Apply newly added snapshot. |
||
| 170 | +279 |
- )+ |
||
| 171 | +280 |
- )+ # Restore initial state ---- |
||
| 172 | -167x - | +281 | +80x |
- } else if (inherits(data(), "error")) {
+ observeEvent(input$snapshot_reset, {
|
| 173 | -7x - | +282 | +2x |
- if (is_shiny_silent_error && !validate_shiny_silent_error) {
+ logger::log_debug("srv_snapshot_manager: snapshot_reset button clicked, restoring snapshot")
|
| 174 | -1x - | +283 | +2x |
- return(NULL)+ s <- "Initial application state" |
| 175 | +284 |
- }- |
- ||
| 176 | -6x - | -
- validate(+ ### Begin restore procedure. ### |
||
| 177 | -6x - | +285 | +2x |
- need(+ snapshot <- snapshot_history()[[s]] |
| 178 | -6x - | +|||
| 286 | +
- FALSE,+ # todo: as.teal_slices looses module-mapping if is not global |
|||
| 179 | -6x - | +287 | +2x |
- sprintf(+ snapshot_state <- as.teal_slices(snapshot) |
| 180 | -6x - | +288 | +2x |
- "Shiny error when executing the `data` module.\n%s\n%s",+ slices_global$slices_set(snapshot_state) |
| 181 | -6x - | +289 | +2x |
- data()$message,+ removeModal() |
| 182 | -6x - | +|||
| 290 | +
- "Check your inputs or contact app developer if error persists."+ ### End restore procedure. ### |
|||
| 183 | +291 |
- )+ }) |
||
| 184 | +292 |
- )+ |
||
| 185 | +293 |
- )+ # Build snapshot table ---- |
||
| 186 | +294 |
- }+ # Create UI elements and server logic for the snapshot table. |
||
| 187 | +295 |
- })+ # Observers must be tracked to avoid duplication and excess reactivity. |
||
| 188 | +296 |
- })+ # Remaining elements are tracked likewise for consistency and a slight speed margin. |
||
| 189 | -+ | |||
| 297 | +80x |
- }+ observers <- reactiveValues() |
||
| 190 | -+ | |||
| 298 | +80x |
-
+ handlers <- reactiveValues() |
||
| 191 | -+ | |||
| 299 | +80x |
-
+ divs <- reactiveValues() |
||
| 192 | +300 |
- #' @keywords internal+ |
||
| 193 | -+ | |||
| 301 | +80x |
- ui_check_class_teal_data <- function(id) {
+ observeEvent(snapshot_history(), {
|
||
| 194 | -77x - | +302 | +70x |
- ns <- NS(id)+ logger::log_debug("srv_snapshot_manager: snapshot history modified, updating snapshot list")
|
| 195 | -77x - | +303 | +70x |
- uiOutput(ns("message"))
+ lapply(names(snapshot_history())[-1L], function(s) {
|
| 196 | -+ | |||
| 304 | +! |
- }+ id_pickme <- sprintf("pickme_%s", make.names(s))
|
||
| 197 | -+ | |||
| 305 | +! |
-
+ id_saveme <- sprintf("saveme_%s", make.names(s))
|
||
| 198 | -+ | |||
| 306 | +! |
- #' @keywords internal+ id_rowme <- sprintf("rowme_%s", make.names(s))
|
||
| 199 | +307 |
- srv_check_class_teal_data <- function(id, data) {
+
|
||
| 200 | -172x - | +|||
| 308 | +
- checkmate::assert_string(id)+ # Observer for restoring snapshot. |
|||
| 201 | -172x - | +|||
| 309 | +! |
- moduleServer(id, function(input, output, session) {
+ if (!is.element(id_pickme, names(observers))) {
|
||
| 202 | -172x - | +|||
| 310 | +! |
- output$message <- renderUI({
+ observers[[id_pickme]] <- observeEvent(input[[id_pickme]], {
|
||
| 203 | -175x - | +|||
| 311 | +
- validate(+ ### Begin restore procedure. ### |
|||
| 204 | -175x - | +|||
| 312 | +! |
- need(+ snapshot <- snapshot_history()[[s]] |
||
| 205 | -175x - | +|||
| 313 | +! |
- inherits(data(), c("teal_data", "error")),
+ snapshot_state <- as.teal_slices(snapshot) |
||
| 206 | -175x - | +|||
| 314 | +
- "Did not receive `teal_data` object. Cannot proceed further."+ |
|||
| 207 | -+ | |||
| 315 | +! |
- )+ slices_global$slices_set(snapshot_state) |
||
| 208 | -+ | |||
| 316 | +! |
- )+ removeModal() |
||
| 209 | +317 |
- })+ ### End restore procedure. ### |
||
| 210 | +318 |
- })+ }) |
||
| 211 | +319 |
- }+ } |
||
| 212 | +320 |
-
+ # Create handler for downloading snapshot. |
||
| 213 | -+ | |||
| 321 | +! |
- #' @keywords internal+ if (!is.element(id_saveme, names(handlers))) {
|
||
| 214 | -+ | |||
| 322 | +! |
- ui_check_shiny_warnings <- function(id) {
+ output[[id_saveme]] <- downloadHandler( |
||
| 215 | -77x - | +|||
| 323 | +! |
- ns <- NS(id)+ filename = function() {
|
||
| 216 | -77x - | +|||
| 324 | +! |
- uiOutput(NS(id, "message"))+ sprintf("teal_snapshot_%s_%s.json", s, Sys.Date())
|
||
| 217 | +325 |
- }+ }, |
||
| 218 | -+ | |||
| 326 | +! |
-
+ content = function(file) {
|
||
| 219 | -+ | |||
| 327 | +! |
- #' @keywords internal+ snapshot <- snapshot_history()[[s]] |
||
| 220 | -+ | |||
| 328 | +! |
- srv_check_shiny_warnings <- function(id, data, modules) {
+ snapshot_state <- as.teal_slices(snapshot) |
||
| 221 | -172x - | +|||
| 329 | +! |
- checkmate::assert_string(id)+ slices_store(tss = snapshot_state, file = file) |
||
| 222 | -172x - | +|||
| 330 | +
- moduleServer(id, function(input, output, session) {
+ } |
|||
| 223 | -172x - | +|||
| 331 | +
- output$message <- renderUI({
+ ) |
|||
| 224 | -175x - | +|||
| 332 | +! |
- if (inherits(data(), "teal_data")) {
+ handlers[[id_saveme]] <- id_saveme |
||
| 225 | -158x - | +|||
| 333 | +
- is_modules_ok <- check_modules_datanames(modules = modules, datanames = ls(teal.code::get_env(data())))+ } |
|||
| 226 | -158x - | +|||
| 334 | +
- if (!isTRUE(is_modules_ok)) {
+ # Create a row for the snapshot table. |
|||
| 227 | -9x - | +|||
| 335 | +! |
- tags$div(+ if (!is.element(id_rowme, names(divs))) {
|
||
| 228 | -9x - | +|||
| 336 | +! |
- class = "teal-output-warning",+ divs[[id_rowme]] <- tags$div( |
||
| 229 | -9x - | +|||
| 337 | +! |
- is_modules_ok$html(+ class = "manager_table_row", |
||
| 230 | -+ | |||
| 338 | +! |
- # Show modules prefix on message only in teal_data_module tab+ tags$span(tags$h5(s)), |
||
| 231 | -9x - | +|||
| 339 | +! |
- grepl(sprintf("data-teal_data_module-%s", id), session$ns(NULL), fixed = TRUE)
+ actionLink(inputId = ns(id_pickme), label = icon("far fa-circle-check"), title = "select"),
|
||
| 232 | -+ | |||
| 340 | +! |
- )+ downloadLink(outputId = ns(id_saveme), label = icon("far fa-save"), title = "save to file")
|
||
| 233 | +341 |
) |
||
| 234 | +342 |
} |
||
| 235 | +343 |
- }+ }) |
||
| 236 | +344 |
}) |
||
| 237 | +345 |
- })+ |
||
| 238 | +346 |
- }+ # Create table to display list of snapshots and their actions. |
||
| 239 | -+ | |||
| 347 | +80x |
-
+ output$snapshot_list <- renderUI({
|
||
| 240 | -+ | |||
| 348 | +70x |
- .trigger_on_success <- function(data) {
+ rows <- rev(reactiveValuesToList(divs)) |
||
| 241 | -172x - | +349 | +70x |
- out <- reactiveVal(NULL)+ if (length(rows) == 0L) {
|
| 242 | -172x - | +350 | +70x |
- observeEvent(data(), {
+ tags$div( |
| 243 | -169x - | +351 | +70x |
- if (inherits(data(), "teal_data")) {
+ class = "manager_placeholder", |
| 244 | -158x - | +352 | +70x |
- if (!identical(data(), out())) {
+ "Snapshots will appear here." |
| 245 | -158x - | +|||
| 353 | +
- out(data())+ ) |
|||
| 246 | +354 |
- }+ } else {
+ |
+ ||
| 355 | +! | +
+ rows |
||
| 247 | +356 |
- }+ } |
||
| 248 | +357 |
- })+ }) |
||
| 249 | +358 | |||
| 250 | -172x - | +359 | +80x |
- out+ snapshot_history |
| 251 | +360 | ++ |
+ })+ |
+ |
| 361 |
}@@ -28719,14 +27162,14 @@ teal coverage - 59.73% |
| 1 |
- #' Create a `tdata` object+ #' App state management. |
||
| 3 |
- #' @description `r lifecycle::badge("superseded")`
+ #' @description |
||
| 4 |
- #'+ #' `r lifecycle::badge("experimental")`
|
||
| 5 |
- #' Recent changes in `teal` cause modules to fail because modules expect a `tdata` object+ #' |
||
| 6 |
- #' to be passed to the `data` argument but instead they receive a `teal_data` object,+ #' Capture and restore the global (app) input state. |
||
| 7 |
- #' which is additionally wrapped in a reactive expression in the server functions.+ #' |
||
| 8 |
- #' In order to easily adapt such modules without a proper refactor,+ #' @details |
||
| 9 |
- #' use this function to downgrade the `data` argument.+ #' This module introduces bookmarks into `teal` apps: the `shiny` bookmarking mechanism becomes enabled |
||
| 10 |
- #'+ #' and server-side bookmarks can be created. |
||
| 11 |
- #' @name tdata+ #' |
||
| 12 |
- #' @param ... ignored+ #' The bookmark manager presents a button with the bookmark icon and is placed in the tab-bar. |
||
| 13 |
- #' @return nothing+ #' When clicked, the button creates a bookmark and opens a modal which displays the bookmark URL. |
||
| 14 |
- NULL+ #' |
||
| 15 |
-
+ #' `teal` does not guarantee that all modules (`teal_module` objects) are bookmarkable. |
||
| 16 |
- #' @rdname tdata+ #' Those that are, have a `teal_bookmarkable` attribute set to `TRUE`. If any modules are not bookmarkable, |
||
| 17 |
- #' @export+ #' the bookmark manager modal displays a warning and the bookmark button displays a flag. |
||
| 18 |
- new_tdata <- function(...) {
+ #' In order to communicate that a external module is bookmarkable, the module developer |
||
| 19 | -! | +
- .deprecate_tdata_msg()+ #' should set the `teal_bookmarkable` attribute to `TRUE`. |
|
| 20 |
- }+ #' |
||
| 21 |
-
+ #' @section Server logic: |
||
| 22 |
- #' @rdname tdata+ #' A bookmark is a URL that contains the app address with a `/?_state_id_=<bookmark_dir>` suffix. |
||
| 23 |
- #' @export+ #' `<bookmark_dir>` is a directory created on the server, where the state of the application is saved. |
||
| 24 |
- tdata2env <- function(...) {
+ #' Accessing the bookmark URL opens a new session of the app that starts in the previously saved state. |
||
| 25 | -! | +
- .deprecate_tdata_msg()+ #' |
|
| 26 |
- }+ #' @section Note: |
||
| 27 |
-
+ #' To enable bookmarking use either: |
||
| 28 |
- #' @rdname tdata+ #' - `shiny` app by using `shinyApp(..., enableBookmarking = "server")` (not supported in `shinytest2`) |
||
| 29 |
- #' @export+ #' - set `options(shiny.bookmarkStore = "server")` before running the app |
||
| 30 |
- get_code_tdata <- function(...) {
+ #' |
||
| 31 | -! | +
- .deprecate_tdata_msg()+ #' |
|
| 32 |
- }+ #' @inheritParams init |
||
| 33 |
-
+ #' |
||
| 34 |
- #' @rdname tdata+ #' @return Invisible `NULL`. |
||
| 35 |
- #' @export+ #' |
||
| 36 |
- join_keys.tdata <- function(...) {
+ #' @aliases bookmark bookmark_manager bookmark_manager_module |
||
| 37 | -! | +
- .deprecate_tdata_msg()+ #' |
|
| 38 |
- }+ #' @name module_bookmark_manager |
||
| 39 |
-
+ #' @rdname module_bookmark_manager |
||
| 40 |
- #' @rdname tdata+ #' |
||
| 41 |
- #' @export+ #' @keywords internal |
||
| 42 |
- get_metadata <- function(...) {
+ #' |
||
| 43 | -! | +
- .deprecate_tdata_msg()+ NULL |
|
| 44 |
- }+ |
||
| 45 |
-
+ #' @rdname module_bookmark_manager |
||
| 46 |
- #' @rdname tdata+ ui_bookmark_panel <- function(id, modules) {
|
||
| 47 | -+ | ! |
- #' @export+ ns <- NS(id) |
| 48 |
- as_tdata <- function(...) {
+
|
||
| 49 | ! |
- .deprecate_tdata_msg()+ bookmark_option <- get_bookmarking_option() |
|
| 50 | -+ | ! |
- }+ is_unbookmarkable <- need_bookmarking(modules) |
| 51 | -+ | ! |
-
+ shinyOptions(bookmarkStore = bookmark_option) |
| 53 |
- .deprecate_tdata_msg <- function() {
+ # Render bookmark warnings count |
||
| 54 | ! |
- lifecycle::deprecate_stop(+ if (!all(is_unbookmarkable) && identical(bookmark_option, "server")) {
|
|
| 55 | ! |
- when = "0.16",+ tags$button( |
|
| 56 | ! |
- what = "tdata()",+ id = ns("do_bookmark"),
|
|
| 57 | ! |
- details = paste(+ class = "btn action-button wunder_bar_button bookmark_manager_button", |
|
| 58 | ! |
- "tdata has been removed in favour of `teal_data`.\n",+ title = "Add bookmark", |
|
| 59 | ! |
- "Please follow migration instructions https://github.com/insightsengineering/teal/discussions/987."+ tags$span( |
|
| 60 | -+ | ! |
- )+ suppressMessages(icon("fas fa-bookmark")),
|
| 61 | -+ | ! |
- )+ if (any(is_unbookmarkable)) {
|
| 62 | -- |
- }- |
-
| 1 | -- |
- #' Filter panel module in teal- |
- ||
| 2 | -- |
- #'- |
- ||
| 3 | -- |
- #' Creates filter panel module from `teal_data` object and returns `teal_data`. It is build in a way- |
- ||
| 4 | -- |
- #' that filter panel changes and anything what happens before (e.g. [`module_init_data`]) is triggering- |
- ||
| 5 | -- |
- #' further reactive events only if something has changed and if the module is visible. Thanks to- |
- ||
| 6 | -- |
- #' this special implementation all modules' data are recalculated only for those modules which are- |
- ||
| 7 | -- |
- #' currently displayed.- |
- ||
| 8 | -- |
- #'- |
- ||
| 9 | -- |
- #' @return A `eventReactive` containing `teal_data` containing filtered objects and filter code.- |
- ||
| 10 | -- |
- #' `eventReactive` triggers only if all conditions are met:- |
- ||
| 11 | -- |
- #' - tab is selected (`is_active`)- |
- ||
| 12 | -- |
- #' - when filters are changed (`get_filter_expr` is different than previous)- |
- ||
| 13 | -- |
- #'- |
- ||
| 14 | -- |
- #' @inheritParams module_teal_module- |
- ||
| 15 | -- |
- #' @param active_datanames (`reactive` returning `character`) this module's data names- |
- ||
| 16 | -+ | ! |
- #' @name module_filter_data+ tags$span( |
|
| 17 | -+ | |||
| 63 | +! |
- #' @keywords internal+ sum(is_unbookmarkable), |
||
| 18 | -+ | |||
| 64 | +! |
- NULL+ class = "badge-warning badge-count text-white bg-danger" |
||
| 19 | +65 |
-
+ ) |
||
| 20 | +66 |
- #' @rdname module_filter_data+ } |
||
| 21 | +67 |
- ui_filter_data <- function(id) {
+ ) |
||
| 22 | -! | +|||
| 68 | +
- ns <- shiny::NS(id)+ ) |
|||
| 23 | -! | +|||
| 69 | +
- uiOutput(ns("panel"))
+ } |
|||
| 24 | +70 |
} |
||
| 25 | +71 | |||
| 26 | +72 |
- #' @rdname module_filter_data+ #' @rdname module_bookmark_manager |
||
| 27 | +73 |
- srv_filter_data <- function(id, datasets, active_datanames, data_rv, is_active) {
+ srv_bookmark_panel <- function(id, modules) {
|
||
| 28 | -76x - | +74 | +80x |
- assert_reactive(datasets)+ checkmate::assert_character(id) |
| 29 | -76x - | +75 | +80x |
- moduleServer(id, function(input, output, session) {
+ checkmate::assert_class(modules, "teal_modules") |
| 30 | -76x - | +76 | +80x |
- active_corrected <- reactive(intersect(active_datanames(), datasets()$datanames()))+ moduleServer(id, function(input, output, session) {
|
| 31 | -+ | |||
| 77 | +80x |
-
+ logger::log_debug("bookmark_manager_srv initializing")
|
||
| 32 | -76x - | +78 | +80x |
- output$panel <- renderUI({
+ ns <- session$ns |
| 33 | -78x - | +79 | +80x |
- req(inherits(datasets(), "FilteredData"))+ bookmark_option <- get_bookmarking_option() |
| 34 | -78x - | +80 | +80x |
- isolate({
+ is_unbookmarkable <- need_bookmarking(modules) |
| 35 | +81 |
- # render will be triggered only when FilteredData object changes (not when filters change)+ |
||
| 36 | +82 |
- # technically it means that teal_data_module needs to be refreshed+ # Set up bookmarking callbacks ---- |
||
| 37 | -78x - | +|||
| 83 | +
- logger::log_debug("srv_filter_panel rendering filter panel.")
+ # Register bookmark exclusions: do_bookmark button to avoid re-bookmarking |
|||
| 38 | -78x - | +84 | +80x |
- if (length(active_corrected())) {
+ setBookmarkExclude(c("do_bookmark"))
|
| 39 | -77x - | +|||
| 85 | +
- datasets()$srv_active("filters", active_datanames = active_corrected)
+ # This bookmark can only be used on the app session. |
|||
| 40 | -77x - | -
- datasets()$ui_active(session$ns("filters"), active_datanames = active_corrected)
- |
- ||
| 41 | -+ | 86 | +80x |
- }+ app_session <- .subset2(session, "parent") |
| 42 | -+ | |||
| 87 | +80x |
- })+ app_session$onBookmarked(function(url) {
|
||
| 43 | -+ | |||
| 88 | +! |
- })+ logger::log_debug("bookmark_manager_srv@onBookmarked: bookmark button clicked, registering bookmark")
|
||
| 44 | -+ | |||
| 89 | +! |
-
+ modal_content <- if (bookmark_option != "server") {
|
||
| 45 | -76x - | +|||
| 90 | +! |
- trigger_data <- .observe_active_filter_changed(datasets, is_active, active_corrected, data_rv)+ msg <- sprintf( |
||
| 46 | -+ | |||
| 91 | +! |
-
+ "Bookmarking has been set to \"%s\".\n%s\n%s", |
||
| 47 | -76x - | +|||
| 92 | +! |
- eventReactive(trigger_data(), {
+ bookmark_option, |
||
| 48 | -79x - | +|||
| 93 | +! |
- .make_filtered_teal_data(modules, data = data_rv(), datasets = datasets(), datanames = active_corrected())+ "Only server-side bookmarking is supported.", |
||
| 49 | -+ | |||
| 94 | +! |
- })+ "Please contact your app developer." |
||
| 50 | +95 |
- })+ ) |
||
| 51 | -+ | |||
| 96 | +! |
- }+ tags$div( |
||
| 52 | -+ | |||
| 97 | +! |
-
+ tags$p(msg, class = "text-warning") |
||
| 53 | +98 |
- #' @rdname module_filter_data+ ) |
||
| 54 | +99 |
- .make_filtered_teal_data <- function(modules, data, datasets = NULL, datanames) {
+ } else {
|
||
| 55 | -79x - | +|||
| 100 | +! |
- data <- eval_code(+ tags$div( |
||
| 56 | -79x - | +|||
| 101 | +! |
- data,+ tags$span( |
||
| 57 | -79x - | +|||
| 102 | +! |
- paste0(+ tags$pre(url) |
||
| 58 | -79x - | +|||
| 103 | +
- ".raw_data <- list2env(list(",
+ ), |
|||
| 59 | -79x - | +|||
| 104 | +! |
- toString(sprintf("%1$s = %1$s", sapply(datanames, as.name))),
+ if (any(is_unbookmarkable)) {
|
||
| 60 | -79x - | +|||
| 105 | +! |
- "))\n",+ bkmb_summary <- rapply2( |
||
| 61 | -79x - | +|||
| 106 | +! |
- "lockEnvironment(.raw_data) # @linksto .raw_data" # this is environment and it is shared by qenvs. CAN'T MODIFY!+ modules_bookmarkable(modules), |
||
| 62 | -+ | |||
| 107 | +! |
- )+ function(x) {
|
||
| 63 | -+ | |||
| 108 | +! |
- )+ if (isTRUE(x)) {
|
||
| 64 | -79x - | +|||
| 109 | +! |
- filtered_code <- .get_filter_expr(datasets = datasets, datanames = datanames)+ "\u2705" # check mark |
||
| 65 | -79x - | +|||
| 110 | +! |
- filtered_teal_data <- .append_evaluated_code(data, filtered_code)+ } else if (isFALSE(x)) {
|
||
| 66 | -79x - | +|||
| 111 | +! |
- filtered_datasets <- sapply(datanames, function(x) datasets$get_data(x, filtered = TRUE), simplify = FALSE)+ "\u274C" # cross mark |
||
| 67 | -79x - | +|||
| 112 | +
- filtered_teal_data <- .append_modified_data(filtered_teal_data, filtered_datasets)+ } else {
|
|||
| 68 | -79x - | +|||
| 113 | +! |
- filtered_teal_data+ "\u2753" # question mark |
||
| 69 | +114 |
- }+ } |
||
| 70 | +115 |
-
+ } |
||
| 71 | +116 |
- #' @rdname module_filter_data+ ) |
||
| 72 | -+ | |||
| 117 | +! |
- .observe_active_filter_changed <- function(datasets, is_active, active_datanames, data_rv) {
+ tags$div( |
||
| 73 | -76x - | +|||
| 118 | +! |
- previous_signature <- reactiveVal(NULL)+ tags$p( |
||
| 74 | -76x - | +|||
| 119 | +! |
- filter_changed <- reactive({
+ icon("fas fa-exclamation-triangle"),
|
||
| 75 | -175x - | +|||
| 120 | +! |
- req(inherits(datasets(), "FilteredData"))+ "Some modules will not be restored when using this bookmark.", |
||
| 76 | -175x - | +|||
| 121 | +! |
- new_signature <- c(+ tags$br(), |
||
| 77 | -175x - | +|||
| 122 | +! |
- teal.code::get_code(data_rv()),+ "Check the list below to see which modules are not bookmarkable.", |
||
| 78 | -175x - | +|||
| 123 | +! |
- .get_filter_expr(datasets = datasets(), datanames = active_datanames())+ class = "text-warning" |
||
| 79 | +124 |
- )- |
- ||
| 80 | -175x - | -
- if (!identical(previous_signature(), new_signature)) {
- |
- ||
| 81 | -84x - | -
- previous_signature(new_signature)+ ), |
||
| 82 | -84x - | +|||
| 125 | +! |
- TRUE+ tags$pre(yaml::as.yaml(bkmb_summary)) |
||
| 83 | +126 |
- } else {
+ ) |
||
| 84 | -91x - | +|||
| 127 | +
- FALSE+ } |
|||
| 85 | +128 |
- }+ ) |
||
| 86 | +129 |
- })+ } |
||
| 87 | +130 | |||
| 88 | -76x - | -
- trigger_data <- reactiveVal(NULL)- |
- ||
| 89 | -76x - | -
- observe({
- |
- ||
| 90 | -188x - | +|||
| 131 | +! |
- if (isTRUE(is_active() && filter_changed())) {
+ showModal( |
||
| 91 | -84x - | +|||
| 132 | +! |
- isolate({
+ modalDialog( |
||
| 92 | -84x - | +|||
| 133 | +! |
- if (is.null(trigger_data())) {
+ id = ns("bookmark_modal"),
|
||
| 93 | -76x - | +|||
| 134 | +! |
- trigger_data(0)+ title = "Bookmarked teal app url", |
||
| 94 | -+ | |||
| 135 | +! |
- } else {
+ modal_content, |
||
| 95 | -8x - | +|||
| 136 | +! |
- trigger_data(trigger_data() + 1)+ easyClose = TRUE |
||
| 96 | +137 |
- }+ ) |
||
| 97 | +138 |
- })+ ) |
||
| 98 | +139 |
- }+ }) |
||
| 99 | +140 |
- })+ |
||
| 100 | +141 |
-
+ # manually trigger bookmarking because of the problems reported on windows with bookmarkButton in teal |
||
| 101 | -76x - | -
- trigger_data- |
- ||
| 102 | -+ | 142 | +80x |
- }+ observeEvent(input$do_bookmark, {
|
| 103 | -+ | |||
| 143 | +! |
-
+ logger::log_debug("bookmark_manager_srv@1 do_bookmark module clicked.")
|
||
| 104 | -+ | |||
| 144 | +! |
- #' @rdname module_filter_data+ session$doBookmark() |
||
| 105 | +145 |
- .get_filter_expr <- function(datasets, datanames) {
- |
- ||
| 106 | -254x - | -
- if (length(datanames)) {
- |
- ||
| 107 | -251x - | -
- teal.slice::get_filter_expr(datasets = datasets, datanames = datanames)+ }) |
||
| 108 | +146 |
- } else {
+
|
||
| 109 | -3x - | +147 | +80x |
- NULL+ invisible(NULL) |
| 110 | +148 |
- }+ }) |
||
| 111 | +149 |
} |
| 1 | +150 |
- #' Filter settings for `teal` applications+ |
||
| 2 | +151 |
- #'+ |
||
| 3 | +152 |
- #' Specify initial filter states and filtering settings for a `teal` app.+ #' @rdname module_bookmark_manager |
||
| 4 | +153 |
- #'+ get_bookmarking_option <- function() {
|
||
| 5 | -+ | |||
| 154 | +80x |
- #' Produces a `teal_slices` object.+ bookmark_option <- getShinyOption("bookmarkStore")
|
||
| 6 | -+ | |||
| 155 | +80x |
- #' The `teal_slice` components will specify filter states that will be active when the app starts.+ if (is.null(bookmark_option) && identical(getOption("shiny.bookmarkStore"), "server")) {
|
||
| 7 | -+ | |||
| 156 | +! |
- #' Attributes (created with the named arguments) will configure the way the app applies filters.+ bookmark_option <- getOption("shiny.bookmarkStore")
|
||
| 8 | +157 |
- #' See argument descriptions for details.+ } |
||
| 9 | -+ | |||
| 158 | +80x |
- #'+ bookmark_option |
||
| 10 | +159 |
- #' @inheritParams teal.slice::teal_slices+ } |
||
| 11 | +160 |
- #'+ |
||
| 12 | +161 |
- #' @param module_specific (`logical(1)`) optional,+ #' @rdname module_bookmark_manager |
||
| 13 | +162 |
- #' - `FALSE` (default) when one filter panel applied to all modules.+ need_bookmarking <- function(modules) {
|
||
| 14 | -+ | |||
| 163 | +80x |
- #' All filters will be shared by all modules.+ unlist(rapply2( |
||
| 15 | -+ | |||
| 164 | +80x |
- #' - `TRUE` when filter panel module-specific.+ modules_bookmarkable(modules), |
||
| 16 | -+ | |||
| 165 | +80x |
- #' Modules can have different set of filters specified - see `mapping` argument.+ Negate(isTRUE) |
||
| 17 | +166 |
- #' @param mapping `r lifecycle::badge("experimental")`
+ )) |
||
| 18 | +167 |
- #' _This is a new feature. Do kindly share your opinions on+ } |
||
| 19 | +168 |
- #' [`teal`'s GitHub repository](https://github.com/insightsengineering/teal/)._+ |
||
| 20 | +169 |
- #'+ |
||
| 21 | +170 |
- #' (named `list`) specifies which filters will be active in which modules on app start.+ # utilities ---- |
||
| 22 | +171 |
- #' Elements should contain character vector of `teal_slice` `id`s (see [`teal.slice::teal_slice`]).+ |
||
| 23 | +172 |
- #' Names of the list should correspond to `teal_module` `label` set in [module()] function.+ #' Restore value from bookmark. |
||
| 24 | +173 |
- #' - `id`s listed under `"global_filters` will be active in all modules.+ #' |
||
| 25 | +174 |
- #' - If missing, all filters will be applied to all modules.+ #' Get value from bookmark or return default. |
||
| 26 | +175 |
- #' - If empty list, all filters will be available to all modules but will start inactive.+ #' |
||
| 27 | +176 |
- #' - If `module_specific` is `FALSE`, only `global_filters` will be active on start.+ #' Bookmarks can store not only inputs but also arbitrary values. |
||
| 28 | +177 |
- #' @param app_id (`character(1)`)+ #' These values are stored by `onBookmark` callbacks and restored by `onBookmarked` callbacks, |
||
| 29 | +178 |
- #' For internal use only, do not set manually.+ #' and they are placed in the `values` environment in the `session$restoreContext` field. |
||
| 30 | +179 |
- #' Added by `init` so that a `teal_slices` can be matched to the app in which it was used.+ #' Using `teal_data_module` makes it impossible to run the callbacks |
||
| 31 | +180 |
- #' Used for verifying snapshots uploaded from file. See `snapshot`.+ #' because the app becomes ready before modules execute and callbacks are registered. |
||
| 32 | +181 |
- #'+ #' In those cases the stored values can still be recovered from the `session` object directly. |
||
| 33 | +182 |
- #' @param x (`list`) of lists to convert to `teal_slices`+ #' |
||
| 34 | +183 |
- #'+ #' Note that variable names in the `values` environment are prefixed with module name space names, |
||
| 35 | +184 |
- #' @return+ #' therefore, when using this function in modules, `value` must be run through the name space function. |
||
| 36 | +185 |
- #' A `teal_slices` object.+ #' |
||
| 37 | +186 |
- #'+ #' @param value (`character(1)`) name of value to restore |
||
| 38 | +187 |
- #' @seealso [`teal.slice::teal_slices`], [`teal.slice::teal_slice`], [slices_store()]+ #' @param default fallback value |
||
| 39 | +188 |
#' |
||
| 40 | +189 |
- #' @examples+ #' @return |
||
| 41 | +190 |
- #' filter <- teal_slices(+ #' In an application restored from a server-side bookmark, |
||
| 42 | +191 |
- #' teal_slice(dataname = "iris", varname = "Species", id = "species"),+ #' the variable specified by `value` from the `values` environment. |
||
| 43 | +192 |
- #' teal_slice(dataname = "iris", varname = "Sepal.Length", id = "sepal_length"),+ #' Otherwise `default`. |
||
| 44 | +193 |
- #' teal_slice(+ #' |
||
| 45 | +194 |
- #' dataname = "iris", id = "long_petals", title = "Long petals", expr = "Petal.Length > 5"+ #' @keywords internal |
||
| 46 | +195 |
- #' ),+ #' |
||
| 47 | +196 |
- #' teal_slice(dataname = "mtcars", varname = "mpg", id = "mtcars_mpg"),+ restoreValue <- function(value, default) { # nolint: object_name.
|
||
| 48 | -+ | |||
| 197 | +160x |
- #' mapping = list(+ checkmate::assert_character("value")
|
||
| 49 | -+ | |||
| 198 | +160x |
- #' module1 = c("species", "sepal_length"),
+ session_default <- shiny::getDefaultReactiveDomain() |
||
| 50 | -+ | |||
| 199 | +160x |
- #' module2 = c("mtcars_mpg"),
+ session_parent <- .subset2(session_default, "parent") |
||
| 51 | -+ | |||
| 200 | +160x |
- #' global_filters = "long_petals"+ session <- if (is.null(session_parent)) session_default else session_parent |
||
| 52 | +201 |
- #' )+ |
||
| 53 | -+ | |||
| 202 | +160x |
- #' )+ if (isTRUE(session$restoreContext$active) && exists(value, session$restoreContext$values, inherits = FALSE)) {
|
||
| 54 | -+ | |||
| 203 | +! |
- #'+ session$restoreContext$values[[value]] |
||
| 55 | +204 |
- #' app <- init(+ } else {
|
||
| 56 | -+ | |||
| 205 | +160x |
- #' data = teal_data(iris = iris, mtcars = mtcars),+ default |
||
| 57 | +206 |
- #' modules = list(+ } |
||
| 58 | +207 |
- #' module("module1"),
+ } |
||
| 59 | +208 |
- #' module("module2")
+
|
||
| 60 | +209 |
- #' ),+ #' Compare bookmarks. |
||
| 61 | +210 |
- #' filter = filter+ #' |
||
| 62 | +211 |
- #' )+ #' Test if two bookmarks store identical state. |
||
| 63 | +212 |
#' |
||
| 64 | +213 |
- #' if (interactive()) {
+ #' `input` environments are compared one variable at a time and if not identical, |
||
| 65 | +214 |
- #' shinyApp(app$ui, app$server)+ #' values in both bookmarks are reported. States of `datatable`s are stripped |
||
| 66 | +215 |
- #' }+ #' of the `time` element before comparing because the time stamp is always different. |
||
| 67 | +216 |
- #'+ #' The contents themselves are not printed as they are large and the contents are not informative. |
||
| 68 | +217 |
- #' @export+ #' Elements present in one bookmark and absent in the other are also reported. |
||
| 69 | +218 |
- teal_slices <- function(...,+ #' Differences are printed as messages. |
||
| 70 | +219 |
- exclude_varnames = NULL,+ #' |
||
| 71 | +220 |
- include_varnames = NULL,+ #' `values` environments are compared with `all.equal`. |
||
| 72 | +221 |
- count_type = NULL,+ #' |
||
| 73 | +222 |
- allow_add = TRUE,+ #' @section How to use: |
||
| 74 | +223 |
- module_specific = FALSE,+ #' Open an application, change relevant inputs (typically, all of them), and create a bookmark. |
||
| 75 | +224 |
- mapping,+ #' Then open that bookmark and immediately create a bookmark of that. |
||
| 76 | +225 |
- app_id = NULL) {
+ #' If restoring bookmarks occurred properly, the two bookmarks should store the same state. |
||
| 77 | -154x - | +|||
| 226 | +
- shiny::isolate({
+ #' |
|||
| 78 | -154x - | +|||
| 227 | +
- checkmate::assert_flag(allow_add)+ #' |
|||
| 79 | -154x - | +|||
| 228 | +
- checkmate::assert_flag(module_specific)+ #' @param book1,book2 bookmark directories stored in `shiny_bookmarks/`; |
|||
| 80 | -50x - | +|||
| 229 | +
- if (!missing(mapping)) checkmate::assert_list(mapping, types = c("character", "NULL"), names = "named")
+ #' default to the two most recently modified directories |
|||
| 81 | -151x - | +|||
| 230 | +
- checkmate::assert_string(app_id, null.ok = TRUE)+ #' |
|||
| 82 | +231 |
-
+ #' @return |
||
| 83 | -151x - | +|||
| 232 | +
- slices <- list(...)+ #' Invisible `NULL` if bookmarks are identical or if there are no bookmarks to test. |
|||
| 84 | -151x - | +|||
| 233 | +
- all_slice_id <- vapply(slices, `[[`, character(1L), "id")+ #' `FALSE` if inconsistencies are detected. |
|||
| 85 | +234 |
-
+ #' |
||
| 86 | -151x - | +|||
| 235 | +
- if (missing(mapping)) {
+ #' @keywords internal |
|||
| 87 | -104x - | +|||
| 236 | +
- mapping <- if (length(all_slice_id)) {
+ #' |
|||
| 88 | -26x - | +|||
| 237 | +
- list(global_filters = all_slice_id)+ bookmarks_identical <- function(book1, book2) {
|
|||
| 89 | -+ | |||
| 238 | +! |
- } else {
+ if (!dir.exists("shiny_bookmarks")) {
|
||
| 90 | -78x - | +|||
| 239 | +! |
- list()+ message("no bookmark directory")
|
||
| 91 | -+ | |||
| 240 | +! |
- }+ return(invisible(NULL)) |
||
| 92 | +241 |
- }+ } |
||
| 93 | +242 | |||
| 94 | -151x - | -
- if (!module_specific) {
- |
- ||
| 95 | -132x - | -
- mapping[setdiff(names(mapping), "global_filters")] <- NULL- |
- ||
| 96 | -+ | |||
| 243 | +! |
- }+ ans <- TRUE |
||
| 97 | +244 | |||
| 98 | -151x - | +|||
| 245 | +! |
- failed_slice_id <- setdiff(unlist(mapping), all_slice_id)+ if (missing(book1) && missing(book2)) {
|
||
| 99 | -151x - | +|||
| 246 | +! |
- if (length(failed_slice_id)) {
+ dirs <- list.dirs("shiny_bookmarks", recursive = FALSE)
|
||
| 100 | -1x - | +|||
| 247 | +! |
- stop(sprintf(+ bookmarks_sorted <- basename(rev(dirs[order(file.mtime(dirs))])) |
||
| 101 | -1x - | +|||
| 248 | +! |
- "Filters in mapping don't match any available filter.\n %s not in %s",+ if (length(bookmarks_sorted) < 2L) {
|
||
| 102 | -1x - | +|||
| 249 | +! |
- toString(failed_slice_id),+ message("no bookmarks to compare")
|
||
| 103 | -1x - | +|||
| 250 | +! |
- toString(all_slice_id)+ return(invisible(NULL)) |
||
| 104 | +251 |
- ))+ } |
||
| 105 | -+ | |||
| 252 | +! |
- }+ book1 <- bookmarks_sorted[2L]+ |
+ ||
| 253 | +! | +
+ book2 <- bookmarks_sorted[1L] |
||
| 106 | +254 |
-
+ } else {
|
||
| 107 | -150x - | +|||
| 255 | +! |
- tss <- teal.slice::teal_slices(+ if (!dir.exists(file.path("shiny_bookmarks", book1))) stop(book1, " not found")
|
||
| 108 | -+ | |||
| 256 | +! |
- ...,+ if (!dir.exists(file.path("shiny_bookmarks", book2))) stop(book2, " not found")
|
||
| 109 | -150x - | +|||
| 257 | +
- exclude_varnames = exclude_varnames,+ } |
|||
| 110 | -150x - | +|||
| 258 | +
- include_varnames = include_varnames,+ |
|||
| 111 | -150x - | +|||
| 259 | +! |
- count_type = count_type,+ book1_input <- readRDS(file.path("shiny_bookmarks", book1, "input.rds"))
|
||
| 112 | -150x - | +|||
| 260 | +! |
- allow_add = allow_add+ book2_input <- readRDS(file.path("shiny_bookmarks", book2, "input.rds"))
|
||
| 113 | +261 |
- )+ |
||
| 114 | -150x - | +|||
| 262 | +! |
- attr(tss, "mapping") <- mapping+ elements_common <- intersect(names(book1_input), names(book2_input)) |
||
| 115 | -150x - | +|||
| 263 | +! |
- attr(tss, "module_specific") <- module_specific+ dt_states <- grepl("_state$", elements_common)
|
||
| 116 | -150x - | +|||
| 264 | +! |
- attr(tss, "app_id") <- app_id+ if (any(dt_states)) {
|
||
| 117 | -150x - | +|||
| 265 | +! |
- class(tss) <- c("modules_teal_slices", class(tss))
+ for (el in elements_common[dt_states]) {
|
||
| 118 | -150x - | +|||
| 266 | +! |
- tss+ book1_input[[el]][["time"]] <- NULL |
||
| 119 | -+ | |||
| 267 | +! |
- })+ book2_input[[el]][["time"]] <- NULL |
||
| 120 | +268 |
- }+ } |
||
| 121 | +269 |
-
+ } |
||
| 122 | +270 | |||
| 123 | -+ | |||
| 271 | +! |
- #' @rdname teal_slices+ identicals <- mapply(identical, book1_input[elements_common], book2_input[elements_common]) |
||
| 124 | -+ | |||
| 272 | +! |
- #' @export+ non_identicals <- names(identicals[!identicals]) |
||
| 125 | -+ | |||
| 273 | +! |
- #' @keywords internal+ compares <- sprintf("$ %s:\t%s --- %s", non_identicals, book1_input[non_identicals], book2_input[non_identicals])
|
||
| 126 | -+ | |||
| 274 | +! |
- #'+ if (length(compares) != 0L) {
|
||
| 127 | -+ | |||
| 275 | +! |
- as.teal_slices <- function(x) { # nolint: object_name.
+ message("common elements not identical: \n", paste(compares, collapse = "\n"))
|
||
| 128 | -12x - | +|||
| 276 | +! |
- checkmate::assert_list(x)+ ans <- FALSE |
||
| 129 | -12x - | +|||
| 277 | +
- lapply(x, checkmate::assert_list, names = "named", .var.name = "list element")+ } |
|||
| 130 | +278 | |||
| 131 | -12x - | +|||
| 279 | +! |
- attrs <- attributes(unclass(x))+ elements_boook1 <- setdiff(names(book1_input), names(book2_input)) |
||
| 132 | -12x - | +|||
| 280 | +! |
- ans <- lapply(x, function(x) if (is.teal_slice(x)) x else as.teal_slice(x))+ if (length(elements_boook1) != 0L) {
|
||
| 133 | -12x - | +|||
| 281 | +! |
- do.call(teal_slices, c(ans, attrs))+ dt_states <- grepl("_state$", elements_boook1)
|
||
| 134 | -+ | |||
| 282 | +! |
- }+ if (any(dt_states)) {
|
||
| 135 | -+ | |||
| 283 | +! |
-
+ for (el in elements_boook1[dt_states]) {
|
||
| 136 | -+ | |||
| 284 | +! |
-
+ if (is.list(book1_input[[el]])) book1_input[[el]] <- "--- data table state ---" |
||
| 137 | +285 |
- #' @rdname teal_slices+ } |
||
| 138 | +286 |
- #' @export+ } |
||
| 139 | -+ | |||
| 287 | +! |
- #' @keywords internal+ excess1 <- sprintf("$ %s:\t%s", elements_boook1, book1_input[elements_boook1])
+ |
+ ||
| 288 | +! | +
+ message("elements only in book1: \n", paste(excess1, collapse = "\n"))
+ |
+ ||
| 289 | +! | +
+ ans <- FALSE |
||
| 140 | +290 |
- #'+ } |
||
| 141 | +291 |
- c.teal_slices <- function(...) {
+
|
||
| 142 | -6x - | +|||
| 292 | +! |
- x <- list(...)+ elements_boook2 <- setdiff(names(book2_input), names(book1_input)) |
||
| 143 | -6x - | +|||
| 293 | +! |
- checkmate::assert_true(all(vapply(x, is.teal_slices, logical(1L))), .var.name = "all arguments are teal_slices")+ if (length(elements_boook2) != 0L) {
|
||
| 144 | -+ | |||
| 294 | +! |
-
+ dt_states <- grepl("_state$", elements_boook1)
|
||
| 145 | -6x - | +|||
| 295 | +! |
- all_attributes <- lapply(x, attributes)+ if (any(dt_states)) {
|
||
| 146 | -6x - | +|||
| 296 | +! |
- all_attributes <- coalesce_r(all_attributes)+ for (el in elements_boook1[dt_states]) {
|
||
| 147 | -6x - | +|||
| 297 | +! |
- all_attributes <- all_attributes[names(all_attributes) != "class"]+ if (is.list(book2_input[[el]])) book2_input[[el]] <- "--- data table state ---" |
||
| 148 | +298 |
-
+ } |
||
| 149 | -6x - | +|||
| 299 | +
- do.call(+ } |
|||
| 150 | -6x - | +|||
| 300 | +! |
- teal_slices,+ excess2 <- sprintf("$ %s:\t%s", elements_boook2, book2_input[elements_boook2])
|
||
| 151 | -6x - | +|||
| 301 | +! |
- c(+ message("elements only in book2: \n", paste(excess2, collapse = "\n"))
|
||
| 152 | -6x - | +|||
| 302 | +! |
- unique(unlist(x, recursive = FALSE)),+ ans <- FALSE |
||
| 153 | -6x - | +|||
| 303 | +
- all_attributes+ } |
|||
| 154 | +304 |
- )+ |
||
| 155 | -+ | |||
| 305 | +! |
- )+ book1_values <- readRDS(file.path("shiny_bookmarks", book1, "values.rds"))
|
||
| 156 | -+ | |||
| 306 | +! |
- }+ book2_values <- readRDS(file.path("shiny_bookmarks", book2, "values.rds"))
|
||
| 157 | +307 | |||
| 158 | -+ | |||
| 308 | +! |
-
+ if (!isTRUE(all.equal(book1_values, book2_values))) {
|
||
| 159 | -+ | |||
| 309 | +! |
- #' Deep copy `teal_slices`+ message("different values detected")
|
||
| 160 | -+ | |||
| 310 | +! |
- #'+ message("choices for numeric filters MAY be different, see RangeFilterState$set_choices")
|
||
| 161 | -+ | |||
| 311 | +! |
- #' it's important to create a new copy of `teal_slices` when+ ans <- FALSE |
||
| 162 | +312 |
- #' starting a new `shiny` session. Otherwise, object will be shared+ } |
||
| 163 | +313 |
- #' by multiple users as it is created in global environment before+ |
||
| 164 | -+ | |||
| 314 | +! |
- #' `shiny` session starts.+ if (ans) message("perfect!")
+ |
+ ||
| 315 | +! | +
+ invisible(NULL) |
||
| 165 | +316 |
- #' @param filter (`teal_slices`)+ } |
||
| 166 | +317 |
- #' @return `teal_slices`+ |
||
| 167 | +318 |
- #' @keywords internal+ |
||
| 168 | +319 |
- deep_copy_filter <- function(filter) {
+ # Replacement for [base::rapply] which doesn't handle NULL values - skips the evaluation |
||
| 169 | -1x - | +|||
| 320 | +
- checkmate::assert_class(filter, "teal_slices")+ # of the function and returns NULL for given element. |
|||
| 170 | -1x - | +|||
| 321 | +
- shiny::isolate({
+ rapply2 <- function(x, f) {
|
|||
| 171 | -1x - | +322 | +185x |
- filter_copy <- lapply(filter, function(slice) {
+ if (inherits(x, "list")) {
|
| 172 | -2x - | +323 | +80x |
- teal.slice::as.teal_slice(as.list(slice))+ lapply(x, rapply2, f = f) |
| 173 | +324 |
- })- |
- ||
| 174 | -1x - | -
- attributes(filter_copy) <- attributes(filter)+ } else {
|
||
| 175 | -1x - | +325 | +105x |
- filter_copy+ f(x) |
| 176 | +326 |
- })+ } |
||
| 177 | +327 |
}@@ -31283,49 +29457,49 @@ teal coverage - 59.73% |
| 1 |
- # This is the main function from teal to be used by the end-users. Although it delegates+ #' Execute and validate `teal_data_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+ #' This is a low level module to handle `teal_data_module` execution and validation. |
|||
| 4 |
- # error messages.+ #' [teal_transform_module()] inherits from [teal_data_module()] so it is handled by this module too. |
|||
| 5 |
-
+ #' [srv_teal()] accepts various `data` objects and eventually they are all transformed to `reactive` |
|||
| 6 |
- #' Create the server and UI function for the `shiny` app+ #' [teal_data()] which is a standard data class in whole `teal` framework. |
|||
| 8 |
- #' @description `r lifecycle::badge("stable")`
+ #' @section data validation: |
|||
| 10 |
- #' End-users: This is the most important function for you to start a+ #' Executed [teal_data_module()] is validated and output is validated for consistency. |
|||
| 11 |
- #' `teal` app that is composed of `teal` modules.+ #' Output `data` is invalid if: |
|||
| 12 |
- #'+ #' 1. [teal_data_module()] is invalid if server doesn't return `reactive`. **Immediately crashes an app!** |
|||
| 13 |
- #' @param data (`teal_data` or `teal_data_module`)+ #' 2. `reactive` throws a `shiny.error` - happens when module creating [teal_data()] fails. |
|||
| 14 |
- #' For constructing the data object, refer to [teal_data()] and [teal_data_module()].+ #' 3. `reactive` returns `qenv.error` - happens when [teal_data()] evaluates a failing code. |
|||
| 15 |
- #' If `datanames` are not set for the `teal_data` object, defaults from the `teal_data` environment will be used.+ #' 4. `reactive` object doesn't return [teal_data()]. |
|||
| 16 |
- #' @param modules (`list` or `teal_modules` or `teal_module`)+ #' 5. [teal_data()] object lacks any `datanames` specified in the `modules` argument. |
|||
| 17 |
- #' Nested list of `teal_modules` or `teal_module` objects or a single+ #' |
|||
| 18 |
- #' `teal_modules` or `teal_module` object. These are the specific output modules which+ #' `teal` (observers in `srv_teal`) always waits to render an app until `reactive` `teal_data` is |
|||
| 19 |
- #' will be displayed in the `teal` application. See [modules()] and [module()] for+ #' returned. If error 2-4 occurs, relevant error message is displayed to the app user. Once the issue is |
|||
| 20 |
- #' more details.+ #' resolved, the app will continue to run. `teal` guarantees that errors in data don't crash the app |
|||
| 21 |
- #' @param filter (`teal_slices`) Optionally,+ #' (except error 1). |
|||
| 22 |
- #' specifies the initial filter using [teal_slices()].+ #' |
|||
| 23 |
- #' @param title (`shiny.tag` or `character(1)`) Optionally,+ #' @param id (`character(1)`) Module id |
|||
| 24 |
- #' the browser window title. Defaults to a title "teal app" with the icon of NEST.+ #' @param data (`reactive teal_data`) |
|||
| 25 |
- #' Can be created using the `build_app_title()` or+ #' @param data_module (`teal_data_module`) |
|||
| 26 |
- #' by passing a valid `shiny.tag` which is a head tag with title and link tag.+ #' @param modules (`teal_modules` or `teal_module`) For `datanames` validation purpose |
|||
| 27 |
- #' @param header (`shiny.tag` or `character(1)`) Optionally,+ #' @param validate_shiny_silent_error (`logical`) If `TRUE`, then `shiny.silent.error` is validated and |
|||
| 28 |
- #' the header of the app.+ #' @param is_transformer_failed (`reactiveValues`) contains `logical` flags named after each transformer. |
|||
| 29 |
- #' @param footer (`shiny.tag` or `character(1)`) Optionally,+ #' Help to determine if any previous transformer failed, so that following transformers can be disabled |
|||
| 30 |
- #' the footer of the app.+ #' and display a generic failure message. |
|||
| 31 |
- #' @param id (`character`) Optionally,+ #' |
|||
| 32 |
- #' a string specifying the `shiny` module id in cases it is used as a `shiny` module+ #' @return `reactive` `teal_data` |
|||
| 33 |
- #' rather than a standalone `shiny` app. This is a legacy feature.+ #' |
|||
| 34 |
- #' @param landing_popup (`teal_module_landing`) Optionally,+ #' @rdname module_teal_data |
|||
| 35 |
- #' a `landing_popup_module` to show up as soon as the teal app is initialized.+ #' @name module_teal_data |
|||
| 36 |
- #'+ #' @keywords internal |
|||
| 37 |
- #' @return Named list containing server and UI functions.+ NULL |
|||
| 38 |
- #'+ |
|||
| 39 |
- #' @export+ #' @rdname module_teal_data |
|||
| 40 |
- #'+ ui_teal_data <- function(id, data_module = function(id) NULL) {
|
|||
| 41 | -+ | ! |
- #' @include modules.R+ checkmate::assert_string(id) |
|
| 42 | -+ | ! |
- #'+ checkmate::assert_function(data_module, args = "id") |
|
| 43 | -+ | ! |
- #' @examples+ ns <- NS(id) |
|
| 44 |
- #' app <- init(+ |
|||
| 45 | -+ | ! |
- #' data = within(+ shiny::tagList( |
|
| 46 | -+ | ! |
- #' teal_data(),+ tags$div(id = ns("wrapper"), data_module(id = ns("data"))),
|
|
| 47 | -+ | ! |
- #' {
+ ui_validate_reactive_teal_data(ns("validate"))
|
|
| 48 |
- #' new_iris <- transform(iris, id = seq_len(nrow(iris)))+ ) |
|||
| 49 |
- #' new_mtcars <- transform(mtcars, id = seq_len(nrow(mtcars)))+ } |
|||
| 50 |
- #' }+ |
|||
| 51 |
- #' ),+ #' @rdname module_teal_data |
|||
| 52 |
- #' modules = modules(+ srv_teal_data <- function(id, |
|||
| 53 |
- #' module(+ data_module = function(id) NULL, |
|||
| 54 |
- #' label = "data source",+ modules = NULL, |
|||
| 55 |
- #' server = function(input, output, session, data) {},
+ validate_shiny_silent_error = TRUE, |
|||
| 56 |
- #' ui = function(id, ...) tags$div(p("information about data source")),
+ is_transformer_failed = reactiveValues()) {
|
|||
| 57 | -+ | 19x |
- #' datanames = "all"+ checkmate::assert_string(id) |
|
| 58 | -+ | 19x |
- #' ),+ checkmate::assert_function(data_module, args = "id") |
|
| 59 | -+ | 19x |
- #' example_module(label = "example teal module"),+ checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"), null.ok = TRUE)
|
|
| 60 | -+ | 19x |
- #' module(+ checkmate::assert_class(is_transformer_failed, "reactivevalues") |
|
| 61 |
- #' "Iris Sepal.Length histogram",+ |
|||
| 62 | -+ | 19x |
- #' server = function(input, output, session, data) {
+ moduleServer(id, function(input, output, session) {
|
|
| 63 | -+ | 19x |
- #' output$hist <- renderPlot(+ logger::log_debug("srv_teal_data initializing.")
|
|
| 64 | -+ | 19x |
- #' hist(data()[["new_iris"]]$Sepal.Length)+ is_transformer_failed[[id]] <- FALSE |
|
| 65 | -+ | 19x |
- #' )+ data_out <- data_module(id = "data") |
|
| 66 | -+ | 19x |
- #' },+ data_handled <- reactive(tryCatch(data_out(), error = function(e) e)) |
|
| 67 | -+ | 19x |
- #' ui = function(id, ...) {
+ observeEvent(data_handled(), {
|
|
| 68 | -+ | 21x |
- #' ns <- NS(id)+ if (!inherits(data_handled(), "teal_data")) {
|
|
| 69 | -+ | 6x |
- #' plotOutput(ns("hist"))
+ is_transformer_failed[[id]] <- TRUE |
|
| 70 |
- #' },+ } else {
|
|||
| 71 | -+ | 15x |
- #' datanames = "new_iris"+ is_transformer_failed[[id]] <- FALSE |
|
| 72 |
- #' )+ } |
|||
| 73 |
- #' ),+ }) |
|||
| 74 |
- #' filter = teal_slices(+ |
|||
| 75 | -+ | 19x |
- #' teal_slice(dataname = "new_iris", varname = "Species"),+ is_previous_failed <- reactive({
|
|
| 76 | -+ | 19x |
- #' teal_slice(dataname = "new_iris", varname = "Sepal.Length"),+ idx_this <- which(names(is_transformer_failed) == id) |
|
| 77 | -+ | 19x |
- #' teal_slice(dataname = "new_mtcars", varname = "cyl"),+ is_transformer_failed_list <- reactiveValuesToList(is_transformer_failed) |
|
| 78 | -+ | 19x |
- #' exclude_varnames = list(new_iris = c("Sepal.Width", "Petal.Width")),
+ idx_failures <- which(unlist(is_transformer_failed_list)) |
|
| 79 | -+ | 19x |
- #' module_specific = TRUE,+ any(idx_failures < idx_this) |
|
| 80 |
- #' mapping = list(+ }) |
|||
| 81 |
- #' `example teal module` = "new_iris Species",+ |
|||
| 82 | -+ | 19x |
- #' `Iris Sepal.Length histogram` = "new_iris Species",+ observeEvent(is_previous_failed(), {
|
|
| 83 | -+ | 19x |
- #' global_filters = "new_mtcars cyl"+ if (is_previous_failed()) {
|
|
| 84 | -+ | ! |
- #' )+ shinyjs::disable("wrapper")
|
|
| 85 |
- #' ),+ } else {
|
|||
| 86 | -+ | 19x |
- #' title = "App title",+ shinyjs::enable("wrapper")
|
|
| 87 |
- #' header = tags$h1("Sample App"),
+ } |
|||
| 88 |
- #' footer = tags$p("Sample footer")
+ }) |
|||
| 89 |
- #' )+ |
|||
| 90 | -+ | 19x |
- #' if (interactive()) {
+ srv_validate_reactive_teal_data( |
|
| 91 | -+ | 19x |
- #' shinyApp(app$ui, app$server)+ "validate", |
|
| 92 | -+ | 19x |
- #' }+ data = data_handled, |
|
| 93 | -+ | 19x |
- #'+ modules = modules, |
|
| 94 | -+ | 19x |
- init <- function(data,+ validate_shiny_silent_error = validate_shiny_silent_error, |
|
| 95 | -+ | 19x |
- modules,+ hide_validation_error = is_previous_failed |
|
| 96 |
- filter = teal_slices(),+ ) |
|||
| 97 |
- title = build_app_title(),+ }) |
|||
| 98 |
- header = tags$p(),+ } |
|||
| 99 |
- footer = tags$p(),+ |
|||
| 100 |
- id = character(0),+ #' @rdname module_teal_data |
|||
| 101 |
- landing_popup = NULL) {
+ ui_validate_reactive_teal_data <- function(id) {
|
|||
| 102 | -11x - | +80x |
- logger::log_debug("init initializing teal app with: data ('{ class(data) }').")
+ ns <- NS(id) |
|
| 103 | -+ | 80x |
-
+ tagList( |
|
| 104 | -+ | 80x |
- # argument checking (independent)+ div( |
|
| 105 | -+ | 80x |
- ## `data`+ id = ns("validate_messages"),
|
|
| 106 | -11x - | +80x |
- if (inherits(data, "TealData")) {
+ class = "teal_validated", |
|
| 107 | -! | +80x |
- lifecycle::deprecate_stop(+ ui_validate_error(ns("silent_error")),
|
|
| 108 | -! | +80x |
- when = "0.15.0",+ ui_check_class_teal_data(ns("class_teal_data")),
|
|
| 109 | -! | +80x |
- what = "init(data)",+ ui_check_shiny_warnings(ns("shiny_warnings"))
|
|
| 110 | -! | +
- paste(+ ), |
||
| 111 | -! | +80x |
- "TealData is no longer supported. Use teal_data() instead.",+ div( |
|
| 112 | -! | +80x |
- "Please follow migration instructions https://github.com/insightsengineering/teal/discussions/988."+ class = "teal_validated", |
|
| 113 | -+ | 80x |
- )+ uiOutput(ns("previous_failed"))
|
|
| 115 |
- }+ ) |
|||
| 116 | -11x - | +
- checkmate::assert_multi_class(data, c("teal_data", "teal_data_module"))
+ } |
||
| 117 | -11x - | +
- checkmate::assert_class(landing_popup, "teal_module_landing", null.ok = TRUE)+ |
||
| 118 |
-
+ #' @rdname module_teal_data |
|||
| 119 |
- ## `modules`+ srv_validate_reactive_teal_data <- function(id, # nolint: object_length |
|||
| 120 | -11x - | +
- checkmate::assert(+ data, |
||
| 121 | -11x - | +
- .var.name = "modules",+ modules = NULL, |
||
| 122 | -11x - | +
- checkmate::check_multi_class(modules, c("teal_modules", "teal_module")),
+ validate_shiny_silent_error = FALSE, |
||
| 123 | -11x - | +
- checkmate::check_list(modules, min.len = 1, any.missing = FALSE, types = c("teal_module", "teal_modules"))
+ hide_validation_error = reactive(FALSE)) {
|
||
| 124 | -+ | 178x |
- )+ checkmate::assert_string(id) |
|
| 125 | -11x - | +178x |
- if (inherits(modules, "teal_module")) {
+ checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"), null.ok = TRUE)
|
|
| 126 | -1x - | +178x |
- modules <- list(modules)+ checkmate::assert_flag(validate_shiny_silent_error) |
|
| 127 |
- }+ |
|||
| 128 | -11x - | +178x |
- if (checkmate::test_list(modules, min.len = 1, any.missing = FALSE, types = c("teal_module", "teal_modules"))) {
+ moduleServer(id, function(input, output, session) {
|
|
| 129 | -5x - | +
- modules <- do.call(teal::modules, modules)+ # there is an empty reactive cycle on `init` and `data_rv` has `shiny.silent.error` class |
||
| 130 | -+ | 178x |
- }+ srv_validate_error("silent_error", data, validate_shiny_silent_error)
|
|
| 131 | -+ | 178x |
-
+ srv_check_class_teal_data("class_teal_data", data)
|
|
| 132 | -+ | 178x |
- ## `filter`+ srv_check_shiny_warnings("shiny_warnings", data, modules)
|
|
| 133 | -11x - | +178x |
- checkmate::assert_class(filter, "teal_slices")+ output$previous_failed <- renderUI({
|
|
| 134 | -+ | 168x |
-
+ if (hide_validation_error()) {
|
|
| 135 | -+ | ! |
- ## all other arguments+ shinyjs::hide("validate_messages")
|
|
| 136 | -10x - | +! |
- checkmate::assert(+ tags$div("One of previous transformers failed. Please fix and continue.", class = "teal-output-warning")
|
|
| 137 | -10x - | +
- .var.name = "title",+ } else {
|
||
| 138 | -10x - | +168x |
- checkmate::check_string(title),+ shinyjs::show("validate_messages")
|
|
| 139 | -10x - | +168x |
- checkmate::check_multi_class(title, c("shiny.tag", "shiny.tag.list", "html"))
+ NULL |
|
| 140 |
- )+ } |
|||
| 141 | -10x - | +
- checkmate::assert(+ }) |
||
| 142 | -10x - | +
- .var.name = "header",+ |
||
| 143 | -10x - | +178x |
- checkmate::check_string(header),+ .trigger_on_success(data) |
|
| 144 | -10x - | +
- checkmate::check_multi_class(header, c("shiny.tag", "shiny.tag.list", "html"))
+ }) |
||
| 145 |
- )+ } |
|||
| 146 | -10x - | +
- checkmate::assert(+ |
||
| 147 | -10x - | +
- .var.name = "footer",+ #' @keywords internal |
||
| 148 | -10x - | +
- checkmate::check_string(footer),+ ui_validate_error <- function(id) {
|
||
| 149 | -10x - | +80x |
- checkmate::check_multi_class(footer, c("shiny.tag", "shiny.tag.list", "html"))
+ ns <- NS(id) |
|
| 150 | -+ | 80x |
- )+ uiOutput(ns("message"))
|
|
| 151 | -10x - | +
- checkmate::assert_character(id, max.len = 1, any.missing = FALSE)+ } |
||
| 153 |
- # log+ #' @keywords internal |
|||
| 154 | -10x - | +
- teal.logger::log_system_info()+ srv_validate_error <- function(id, data, validate_shiny_silent_error) {
|
||
| 155 | -+ | 178x |
-
+ checkmate::assert_string(id) |
|
| 156 | -+ | 178x |
- # argument transformations+ checkmate::assert_flag(validate_shiny_silent_error) |
|
| 157 | -+ | 178x |
- ## `modules` - landing module+ moduleServer(id, function(input, output, session) {
|
|
| 158 | -10x - | +178x |
- landing <- extract_module(modules, "teal_module_landing")+ output$message <- renderUI({
|
|
| 159 | -10x - | +181x |
- if (length(landing) == 1L) {
+ is_shiny_silent_error <- inherits(data(), "shiny.silent.error") && identical(data()$message, "") |
|
| 160 | -! | +175x |
- landing_popup <- landing[[1L]]+ if (inherits(data(), "qenv.error")) {
|
|
| 161 | -! | +2x |
- modules <- drop_module(modules, "teal_module_landing")+ validate( |
|
| 162 | -! | +2x |
- lifecycle::deprecate_soft(+ need( |
|
| 163 | -! | +2x |
- when = "0.15.3",+ FALSE, |
|
| 164 | -! | +2x |
- what = "landing_popup_module()",+ paste( |
|
| 165 | -! | +2x |
- details = paste(+ "Error when executing the `data` module:", |
|
| 166 | -! | +2x |
- "Pass `landing_popup_module` to the `landing_popup` argument of the `init` ",+ strip_style(paste(data()$message, collapse = "\n")), |
|
| 167 | -! | +2x |
- "instead of wrapping it into `modules()` and passing to the `modules` argument"+ "\nCheck your inputs or contact app developer if error persists.", |
|
| 168 | -+ | 2x |
- )+ collapse = "\n" |
|
| 169 |
- )+ ) |
|||
| 170 | -10x - | +
- } else if (length(landing) > 1L) {
+ ) |
||
| 171 | -! | +
- stop("Only one `landing_popup_module` can be used.")
+ ) |
||
| 172 | -+ | 173x |
- }+ } else if (inherits(data(), "error")) {
|
|
| 173 | -+ | 7x |
-
+ if (is_shiny_silent_error && !validate_shiny_silent_error) {
|
|
| 174 | -+ | 1x |
- ## `filter` - set app_id attribute unless present (when restoring bookmark)+ return(NULL) |
|
| 175 | -10x - | +
- if (is.null(attr(filter, "app_id", exact = TRUE))) attr(filter, "app_id") <- create_app_id(data, modules)+ } |
||
| 176 | -+ | 6x |
-
+ validate( |
|
| 177 | -+ | 6x |
- ## `filter` - convert teal.slice::teal_slices to teal::teal_slices+ need( |
|
| 178 | -10x - | +6x |
- filter <- as.teal_slices(as.list(filter))+ FALSE, |
|
| 179 | -+ | 6x |
-
+ sprintf( |
|
| 180 | -+ | 6x |
- # argument checking (interdependent)+ "Shiny error when executing the `data` module.\n%s\n%s", |
|
| 181 | -+ | 6x |
- ## `filter` - `modules`+ data()$message, |
|
| 182 | -10x - | +6x |
- if (isTRUE(attr(filter, "module_specific"))) {
+ "Check your inputs or contact app developer if error persists." |
|
| 183 | -! | +
- module_names <- unlist(c(module_labels(modules), "global_filters"))+ ) |
||
| 184 | -! | +
- failed_mod_names <- setdiff(names(attr(filter, "mapping")), module_names)+ ) |
||
| 185 | -! | +
- if (length(failed_mod_names)) {
+ ) |
||
| 186 | -! | +
- stop(+ } |
||
| 187 | -! | +
- sprintf(+ }) |
||
| 188 | -! | +
- "Some module names in the mapping arguments don't match module labels.\n %s not in %s",+ }) |
||
| 189 | -! | +
- toString(failed_mod_names),+ } |
||
| 190 | -! | +
- toString(unique(module_names))+ |
||
| 191 |
- )+ |
|||
| 192 |
- )+ #' @keywords internal |
|||
| 193 |
- }+ ui_check_class_teal_data <- function(id) {
|
|||
| 194 | -+ | 80x |
-
+ ns <- NS(id) |
|
| 195 | -! | +80x |
- if (anyDuplicated(module_names)) {
+ uiOutput(ns("message"))
|
|
| 196 |
- # In teal we are able to set nested modules with duplicated label.+ } |
|||
| 197 |
- # Because mapping argument bases on the relationship between module-label and filter-id,+ |
|||
| 198 |
- # it is possible that module-label in mapping might refer to multiple teal_module (identified by the same label)+ #' @keywords internal |
|||
| 199 | -! | +
- stop(+ srv_check_class_teal_data <- function(id, data) {
|
||
| 200 | -! | +178x |
- sprintf(+ checkmate::assert_string(id) |
|
| 201 | -! | +178x |
- "Module labels should be unique when teal_slices(mapping = TRUE). Duplicated labels:\n%s ",+ moduleServer(id, function(input, output, session) {
|
|
| 202 | -! | +178x |
- toString(module_names[duplicated(module_names)])+ output$message <- renderUI({
|
|
| 203 | -+ | 181x |
- )+ validate( |
|
| 204 | -+ | 181x |
- )+ need( |
|
| 205 | -+ | 181x |
- }+ inherits(data(), c("teal_data", "error")),
|
|
| 206 | -+ | 181x |
- }+ "Did not receive `teal_data` object. Cannot proceed further." |
|
| 207 |
-
+ ) |
|||
| 208 |
- ## `data` - `modules`+ ) |
|||
| 209 | -10x - | +
- if (inherits(data, "teal_data")) {
+ }) |
||
| 210 | -9x - | +
- if (length(ls(teal.code::get_env(data))) == 0) {
+ }) |
||
| 211 | -1x - | +
- stop("The environment of `data` is empty.")
+ } |
||
| 212 |
- }+ |
|||
| 213 |
-
+ #' @keywords internal |
|||
| 214 | -8x - | +
- is_modules_ok <- check_modules_datanames(modules, ls(teal.code::get_env(data)))+ ui_check_shiny_warnings <- function(id) {
|
||
| 215 | -8x - | +80x |
- if (!isTRUE(is_modules_ok) && length(unlist(extract_transformers(modules))) == 0) {
+ ns <- NS(id) |
|
| 216 | -1x - | +80x |
- lapply(is_modules_ok$string, warning, call. = FALSE)+ uiOutput(NS(id, "message")) |
|
| 217 |
- }+ } |
|||
| 219 | -8x - | +
- is_filter_ok <- check_filter_datanames(filter, ls(teal.code::get_env(data)))+ #' @keywords internal |
||
| 220 | -8x - | +
- if (!isTRUE(is_filter_ok)) {
+ srv_check_shiny_warnings <- function(id, data, modules) {
|
||
| 221 | -1x - | +178x |
- warning(is_filter_ok)+ checkmate::assert_string(id) |
|
| 222 | -+ | 178x |
- # we allow app to continue if applied filters are outside+ moduleServer(id, function(input, output, session) {
|
|
| 223 | -+ | 178x |
- # of possible data range+ output$message <- renderUI({
|
|
| 224 | -+ | 181x |
- }+ if (inherits(data(), "teal_data")) {
|
|
| 225 | -+ | 164x |
- }+ is_modules_ok <- check_modules_datanames_html( |
|
| 226 | -+ | 164x |
-
+ modules = modules, datanames = ls(teal.code::get_env(data())) |
|
| 227 | -9x - | +
- reporter <- teal.reporter::Reporter$new()$set_id(attr(filter, "app_id"))+ ) |
||
| 228 | -9x - | +164x |
- if (is_arg_used(modules, "reporter") && length(extract_module(modules, "teal_module_previewer")) == 0) {
+ if (!isTRUE(is_modules_ok)) {
|
|
| 229 | -! | +15x |
- modules <- append_module(+ tags$div(is_modules_ok, class = "teal-output-warning") |
|
| 230 | -! | +
- modules,+ } |
||
| 231 | -! | +
- reporter_previewer_module(server_args = list(previewer_buttons = c("download", "reset")))
+ } |
||
| 232 |
- )+ }) |
|||
| 233 |
- }+ }) |
|||
| 234 |
-
+ } |
|||
| 235 | -9x - | +
- ns <- NS(id)+ |
||
| 236 |
- # Note: UI must be a function to support bookmarking.+ .trigger_on_success <- function(data) {
|
|||
| 237 | -9x - | +178x |
- res <- list(+ out <- reactiveVal(NULL) |
|
| 238 | -9x - | +178x |
- ui = function(request) {
+ observeEvent(data(), {
|
|
| 239 | -! | +175x |
- ui_teal(+ if (inherits(data(), "teal_data")) {
|
|
| 240 | -! | -
- id = ns("teal"),
- |
- ||
| 241 | -! | -
- modules = modules,- |
- ||
| 242 | -! | -
- title = title,- |
- ||
| 243 | -! | -
- header = header,- |
- ||
| 244 | -! | -
- footer = footer- |
- ||
| 245 | -- |
- )- |
- ||
| 246 | -+ | 164x |
- },+ if (!identical(data(), out())) {
|
|
| 247 | -9x - | -
- server = function(input, output, session) {
- |
- ||
| 248 | -! | -
- if (!is.null(landing_popup)) {
- |
- ||
| 249 | -! | +241 | +164x |
- do.call(landing_popup$server, c(list(id = "landing_module_shiny_id"), landing_popup$server_args))+ out(data()) |
| 250 | +242 |
} |
||
| 251 | -! | -
- srv_teal(id = ns("teal"), data = data, modules = modules, filter = deep_copy_filter(filter))
- |
- ||
| 252 | +243 |
} |
||
| 253 | -- |
- )- |
- ||
| 254 | +244 | - - | -||
| 255 | -9x - | -
- logger::log_debug("init teal app has been initialized.")
+ }) |
||
| 256 | +245 | |||
| 257 | -9x - | +246 | +178x |
- res+ out |
| 258 | +247 |
}@@ -33145,14 +31192,14 @@ teal coverage - 59.73% |
| 1 |
- #' An example `teal` module+ #' Generate lockfile for application's environment reproducibility |
||
| 3 |
- #' `r lifecycle::badge("experimental")`
+ #' @param lockfile_path (`character`) path to the lockfile. |
||
| 5 |
- #' @inheritParams teal_modules+ #' @section Different ways of creating lockfile: |
||
| 6 |
- #' @return A `teal` module which can be included in the `modules` argument to [init()].+ #' `teal` leverages [renv::snapshot()], which offers multiple methods for lockfile creation. |
||
| 7 |
- #' @examples+ #' |
||
| 8 |
- #' app <- init(+ #' - **Working directory lockfile**: `teal`, by default, will create an `implicit` type lockfile that uses |
||
| 9 |
- #' data = teal_data(IRIS = iris, MTCARS = mtcars),+ #' `renv::dependencies()` to detect all R packages in the current project's working directory. |
||
| 10 |
- #' modules = example_module()+ #' - **`DESCRIPTION`-based lockfile**: To generate a lockfile based on a `DESCRIPTION` file in your working |
||
| 11 |
- #' )+ #' directory, set `renv::settings$snapshot.type("explicit")`. The naming convention for `type` follows
|
||
| 12 |
- #' if (interactive()) {
+ #' `renv::snapshot()`. For the `"explicit"` type, refer to `renv::settings$package.dependency.fields()` for the |
||
| 13 |
- #' shinyApp(app$ui, app$server)+ #' `DESCRIPTION` fields included in the lockfile. |
||
| 14 |
- #' }+ #' - **Custom files-based lockfile**: To specify custom files as the basis for the lockfile, set |
||
| 15 |
- #' @export+ #' `renv::settings$snapshot.type("custom")` and configure the `renv.snapshot.filter` option.
|
||
| 16 |
- example_module <- function(label = "example teal module", datanames = "all", transformers = list()) {
+ #' |
||
| 17 | -37x - | +
- checkmate::assert_string(label)+ #' @section lockfile usage: |
|
| 18 | -37x - | +
- ans <- module(+ #' After creating the lockfile, you can restore the application's environment using `renv::restore()`. |
|
| 19 | -37x - | +
- label,+ #' |
|
| 20 | -37x - | +
- server = function(id, data) {
+ #' @seealso [renv::snapshot()], [renv::restore()]. |
|
| 21 | -2x - | +
- checkmate::assert_class(isolate(data()), "teal_data")+ #' |
|
| 22 | -2x - | +
- moduleServer(id, function(input, output, session) {
+ #' @return `NULL` |
|
| 23 | -2x - | +
- datanames_rv <- reactive(ls(teal.code::get_env((req(data())))))+ #' |
|
| 24 | -2x - | +
- observeEvent(datanames_rv(), {
+ #' @name module_teal_lockfile |
|
| 25 | -2x - | +
- selected <- input$dataname+ #' @rdname module_teal_lockfile |
|
| 26 | -2x - | +
- if (identical(selected, "")) {
+ #' |
|
| 27 | -! | +
- selected <- restoreInput(session$ns("dataname"), NULL)
+ #' @keywords internal |
|
| 28 | -2x - | +
- } else if (isFALSE(selected %in% datanames_rv())) {
+ NULL |
|
| 29 | -! | +
- selected <- datanames_rv()[1]+ |
|
| 30 |
- }+ #' @rdname module_teal_lockfile |
||
| 31 | -2x - | +
- updateSelectInput(+ ui_teal_lockfile <- function(id) {
|
|
| 32 | -2x - | +! |
- session = session,+ ns <- NS(id) |
| 33 | -2x - | +! |
- inputId = "dataname",+ shiny::tagList( |
| 34 | -2x - | +! |
- choices = datanames_rv(),+ tags$span("", id = ns("lockFileStatus")),
|
| 35 | -2x - | +! |
- selected = selected+ shinyjs::disabled(downloadLink(ns("lockFileLink"), "Download lockfile"))
|
| 36 |
- )+ ) |
||
| 37 |
- })+ } |
||
| 39 | -2x - | +
- output$text <- renderPrint({
+ #' @rdname module_teal_lockfile |
|
| 40 | -2x - | +
- req(input$dataname)+ srv_teal_lockfile <- function(id) {
|
|
| 41 | -! | +81x |
- data()[[input$dataname]]+ moduleServer(id, function(input, output, session) {
|
| 42 | -+ | 81x |
- })+ logger::log_debug("Initialize srv_teal_lockfile.")
|
| 43 | -+ | 81x |
-
+ enable_lockfile_download <- function() {
|
| 44 | -2x - | +! |
- teal.widgets::verbatim_popup_srv(+ shinyjs::html("lockFileStatus", "Application lockfile ready.")
|
| 45 | -2x - | +! |
- id = "rcode",+ shinyjs::hide("lockFileStatus", anim = TRUE)
|
| 46 | -2x - | +! |
- verbatim_content = reactive(teal.code::get_code(data())),+ shinyjs::enable("lockFileLink")
|
| 47 | -2x - | +! |
- title = "Example Code"+ output$lockFileLink <- shiny::downloadHandler( |
| 48 | -+ | ! |
- )+ filename = function() {
|
| 49 | -+ | ! |
- })+ "renv.lock" |
| 50 |
- },+ }, |
||
| 51 | -37x - | +! |
- ui = function(id) {
+ content = function(file) {
|
| 52 | ! |
- ns <- NS(id)+ file.copy(lockfile_path, file) |
|
| 53 | ! |
- teal.widgets::standard_layout(+ file |
|
| 54 | -! | +
- output = verbatimTextOutput(ns("text")),
+ }, |
|
| 55 | ! |
- encoding = tags$div(+ contentType = "application/json" |
|
| 56 | -! | +
- selectInput(ns("dataname"), "Choose a dataset", choices = NULL),
+ ) |
|
| 57 | -! | +
- teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
+ } |
|
| 58 | -+ | 81x |
- )+ disable_lockfile_download <- function() {
|
| 59 | -+ | ! |
- )+ warning("Lockfile creation failed.", call. = FALSE)
|
| 60 | -+ | ! |
- },+ shinyjs::html("lockFileStatus", "Lockfile creation failed.")
|
| 61 | -37x - | +! |
- datanames = datanames,+ shinyjs::hide("lockFileLink")
|
| 62 | -37x - | +
- transformers = transformers+ } |
|
| 63 |
- )+ |
||
| 64 | -37x - | +81x |
- attr(ans, "teal_bookmarkable") <- TRUE+ shiny::onStop(function() {
|
| 65 | -37x - | +81x |
- ans+ if (file.exists(lockfile_path) && !shiny::isRunning()) {
|
| 66 | -- |
- }- |
-
| 1 | -+ | 1x |
- setOldClass("teal_data_module")
+ logger::log_debug("Removing lockfile after shutting down the app")
|
|
| 2 | -+ | |||
| 67 | +1x |
-
+ file.remove(lockfile_path) |
||
| 3 | +68 |
- #' Evaluate code on `teal_data_module`+ } |
||
| 4 | +69 |
- #'+ }) |
||
| 5 | +70 |
- #' @details+ |
||
| 6 | -+ | |||
| 71 | +81x |
- #' `eval_code` evaluates given code in the environment of the `teal_data` object created by the `teal_data_module`.+ lockfile_path <- "teal_app.lock" |
||
| 7 | -+ | |||
| 72 | +81x |
- #' The code is added to the `@code` slot of the `teal_data`.+ mode <- getOption("teal.lockfile.mode", default = "")
|
||
| 8 | +73 |
- #'+ |
||
| 9 | -+ | |||
| 74 | +81x |
- #' @param object (`teal_data_module`)+ if (!(mode %in% c("auto", "enabled", "disabled"))) {
|
||
| 10 | -+ | |||
| 75 | +! |
- #' @inheritParams teal.code::eval_code+ stop("'teal.lockfile.mode' option can only be one of \"auto\", \"disabled\" or \"disabled\". ")
|
||
| 11 | +76 |
- #'+ } |
||
| 12 | +77 |
- #' @return+ |
||
| 13 | -+ | |||
| 78 | +81x |
- #' `eval_code` returns a `teal_data_module` object with a delayed evaluation of `code` when the module is run.+ if (mode == "disabled") {
|
||
| 14 | -+ | |||
| 79 | +1x |
- #'+ logger::log_debug("'teal.lockfile.mode' option is set to 'disabled'. Hiding lockfile download button.")
|
||
| 15 | -+ | |||
| 80 | +1x |
- #' @examples+ shinyjs::hide("lockFileLink")
|
||
| 16 | -+ | |||
| 81 | +1x |
- #' eval_code(tdm, "dataset1 <- subset(dataset1, Species == 'virginica')")+ return(NULL) |
||
| 17 | +82 |
- #'+ } |
||
| 18 | +83 |
- #' @include teal_data_module.R+ |
||
| 19 | -+ | |||
| 84 | +80x |
- #' @name eval_code+ if (file.exists(lockfile_path)) {
|
||
| 20 | -+ | |||
| 85 | +! |
- #' @rdname teal_data_module+ logger::log_debug("Lockfile has already been created for this app - skipping automatic creation.")
|
||
| 21 | -+ | |||
| 86 | +! |
- #' @aliases eval_code,teal_data_module,character-method+ enable_lockfile_download() |
||
| 22 | -+ | |||
| 87 | +! |
- #' @aliases eval_code,teal_data_module,language-method+ return(NULL) |
||
| 23 | +88 |
- #' @aliases eval_code,teal_data_module,expression-method+ } |
||
| 24 | +89 |
- #'+ |
||
| 25 | -+ | |||
| 90 | +80x |
- #' @importFrom methods setMethod+ if (mode == "auto" && .is_disabled_lockfile_scenario()) {
|
||
| 26 | -+ | |||
| 91 | +79x |
- #' @importMethodsFrom teal.code eval_code+ logger::log_debug( |
||
| 27 | -+ | |||
| 92 | +79x |
- #'+ "Automatic lockfile creation disabled. Execution scenario satisfies teal:::.is_disabled_lockfile_scenario()." |
||
| 28 | +93 |
- setMethod("eval_code", signature = c("teal_data_module", "character"), function(object, code) {
- |
- ||
| 29 | -9x - | -
- teal_data_module(+ ) |
||
| 30 | -9x - | +94 | +79x |
- ui = function(id) {
+ shinyjs::hide("lockFileLink")
|
| 31 | -1x - | +95 | +79x |
- ns <- NS(id)+ return(NULL) |
| 32 | -1x - | +|||
| 96 | +
- object$ui(ns("mutate_inner"))
+ } |
|||
| 33 | +97 |
- },+ |
||
| 34 | -9x - | +98 | +1x |
- server = function(id) {
+ if (!.is_lockfile_deps_installed()) {
|
| 35 | -7x - | +|||
| 99 | +! |
- moduleServer(id, function(input, output, session) {
+ warning("Automatic lockfile creation disabled. `mirai` and `renv` packages must be installed.")
|
||
| 36 | -7x - | +|||
| 100 | +! |
- teal_data_rv <- object$server("mutate_inner")
+ shinyjs::hide("lockFileLink")
|
||
| 37 | -6x - | +|||
| 101 | +! |
- td <- eventReactive(teal_data_rv(),+ return(NULL) |
||
| 38 | +102 |
- {
- |
- ||
| 39 | -6x - | -
- if (inherits(teal_data_rv(), c("teal_data", "qenv.error"))) {
+ } |
||
| 40 | -4x - | +|||
| 103 | +
- eval_code(teal_data_rv(), code)+ |
|||
| 41 | +104 |
- } else {
+ # - Will be run only if the lockfile doesn't exist (see the if-s above) |
||
| 42 | -2x - | +|||
| 105 | +
- teal_data_rv()+ # - We render to the tempfile because the process might last after session is closed and we don't |
|||
| 43 | +106 |
- }+ # want to make a "teal_app.renv" then. This is why we copy only during active session. |
||
| 44 | -+ | |||
| 107 | +1x |
- },+ process <- .teal_lockfile_process_invoke(lockfile_path) |
||
| 45 | -6x - | +108 | +1x |
- ignoreNULL = FALSE+ observeEvent(process$status(), {
|
| 46 | -+ | |||
| 109 | +! |
- )+ if (process$status() %in% c("initial", "running")) {
|
||
| 47 | -6x - | +|||
| 110 | +! |
- td+ shinyjs::html("lockFileStatus", "Creating lockfile...")
|
||
| 48 | -+ | |||
| 111 | +! |
- })+ } else if (process$status() == "success") {
|
||
| 49 | -+ | |||
| 112 | +! |
- }+ result <- process$result() |
||
| 50 | -+ | |||
| 113 | +! |
- )+ if (any(grepl("Lockfile written to", result$out))) {
|
||
| 51 | -+ | |||
| 114 | +! |
- })+ logger::log_debug("Lockfile containing { length(result$res$Packages) } packages created.")
|
||
| 52 | -+ | |||
| 115 | +! |
-
+ if (any(grepl("(WARNING|ERROR):", result$out))) {
|
||
| 53 | -+ | |||
| 116 | +! |
- setMethod("eval_code", signature = c("teal_data_module", "language"), function(object, code) {
+ warning("Lockfile created with warning(s) or error(s):", call. = FALSE)
|
||
| 54 | -1x - | +|||
| 117 | +! |
- eval_code(object, code = paste(lang2calls(code), collapse = "\n"))+ for (i in result$out) {
|
||
| 55 | -+ | |||
| 118 | +! |
- })+ warning(i, call. = FALSE) |
||
| 56 | +119 |
-
+ } |
||
| 57 | +120 |
- setMethod("eval_code", signature = c("teal_data_module", "expression"), function(object, code) {
- |
- ||
| 58 | -2x - | -
- eval_code(object, code = paste(lang2calls(code), collapse = "\n"))+ } |
||
| 59 | -+ | |||
| 121 | +! |
- })+ enable_lockfile_download() |
| 1 | +122 |
- #' Module to transform `reactive` `teal_data`+ } else {
|
||
| 2 | -+ | |||
| 123 | +! |
- #'+ disable_lockfile_download() |
||
| 3 | +124 |
- #' Module calls multiple [`module_teal_data`] in sequence so that `reactive teal_data` output+ } |
||
| 4 | -+ | |||
| 125 | +! |
- #' from one module is handed over to the following module's input.+ } else if (process$status() == "error") {
|
||
| 5 | -+ | |||
| 126 | +! |
- #'+ disable_lockfile_download() |
||
| 6 | +127 |
- #' @inheritParams module_teal_data+ } |
||
| 7 | +128 |
- #' @inheritParams teal_modules+ }) |
||
| 8 | +129 |
- #' @return `reactive` `teal_data`+ |
||
| 9 | -+ | |||
| 130 | +1x |
- #'+ NULL |
||
| 10 | +131 |
- #'+ }) |
||
| 11 | +132 |
- #' @name module_transform_data+ } |
||
| 12 | +133 |
- #' @keywords internal+ |
||
| 13 | +134 |
- NULL+ utils::globalVariables(c("opts", "sysenv", "libpaths", "wd", "lockfilepath", "run")) # needed for mirai call
|
||
| 14 | +135 |
-
+ #' @rdname module_teal_lockfile |
||
| 15 | +136 |
- #' @rdname module_transform_data+ .teal_lockfile_process_invoke <- function(lockfile_path) {
|
||
| 16 | -+ | |||
| 137 | +1x |
- ui_transform_data <- function(id, transformers = list(), class = "well") {
+ mirai_obj <- NULL |
||
| 17 | -! | +|||
| 138 | +1x |
- checkmate::assert_string(id)+ process <- shiny::ExtendedTask$new(function() {
|
||
| 18 | -! | +|||
| 139 | +1x |
- checkmate::assert_list(transformers, "teal_transform_module")+ m <- mirai::mirai( |
||
| 19 | +140 |
-
+ {
|
||
| 20 | -! | +|||
| 141 | +1x |
- ns <- NS(id)+ options(opts) |
||
| 21 | -! | +|||
| 142 | +1x |
- labels <- lapply(transformers, function(x) attr(x, "label"))+ do.call(Sys.setenv, sysenv) |
||
| 22 | -! | +|||
| 143 | +1x |
- ids <- get_unique_labels(labels)+ .libPaths(libpaths) |
||
| 23 | -! | +|||
| 144 | +1x |
- names(transformers) <- ids+ setwd(wd) |
||
| 24 | -+ | |||
| 145 | +1x |
-
+ run(lockfile_path = lockfile_path) |
||
| 25 | -! | +|||
| 146 | +
- lapply(+ }, |
|||
| 26 | -! | +|||
| 147 | +1x |
- names(transformers),+ run = .renv_snapshot, |
||
| 27 | -! | +|||
| 148 | +1x |
- function(name) {
+ lockfile_path = lockfile_path, |
||
| 28 | -! | +|||
| 149 | +1x |
- data_mod <- transformers[[name]]+ opts = options(), |
||
| 29 | -! | +|||
| 150 | +1x |
- wrapper_id <- ns(sprintf("wrapper_%s", name))
+ libpaths = .libPaths(), |
||
| 30 | -! | +|||
| 151 | +1x |
- div( # todo: accordion?+ sysenv = as.list(Sys.getenv()), |
||
| 31 | -+ | |||
| 152 | +1x |
- # class .teal_validated changes the color of the boarder on error in ui_validate_reactive_teal_data+ wd = getwd() |
||
| 32 | +153 |
- # For details see tealValidate.js file.- |
- ||
| 33 | -! | -
- class = c(class, "teal_validated"),- |
- ||
| 34 | -! | -
- title = attr(data_mod, "label"),- |
- ||
| 35 | -! | -
- tags$span(+ ) |
||
| 36 | -! | +|||
| 154 | +1x |
- class = "text-primary mb-4",+ mirai_obj <<- m |
||
| 37 | -! | +|||
| 155 | +1x |
- icon("fas fa-square-pen"),
+ m |
||
| 38 | -! | +|||
| 156 | +
- attr(data_mod, "label")+ }) |
|||
| 39 | +157 |
- ),+ |
||
| 40 | -! | +|||
| 158 | +1x |
- tags$i(+ shiny::onStop(function() {
|
||
| 41 | -! | +|||
| 159 | +1x |
- class = "remove pull-right fa fa-angle-down",+ if (mirai::unresolved(mirai_obj)) {
|
||
| 42 | +160 | ! |
- style = "cursor: pointer;",+ logger::log_debug("Terminating a running lockfile process...")
|
|
| 43 | +161 | ! |
- title = "fold/expand transform panel",+ mirai::stop_mirai(mirai_obj) # this doesn't stop running - renv will be created even if session is closed |
|
| 44 | -! | +|||
| 162 | +
- onclick = sprintf("togglePanelItems(this, '%s', 'fa-angle-right', 'fa-angle-down');", wrapper_id)
+ } |
|||
| 45 | +163 |
- ),+ }) |
||
| 46 | -! | +|||
| 164 | +
- div(+ |
|||
| 47 | -! | +|||
| 165 | +1x |
- id = wrapper_id,+ suppressWarnings({ # 'package:stats' may not be available when loading
|
||
| 48 | -! | +|||
| 166 | +1x |
- ui_teal_data(id = ns(name), data_module = transformers[[name]]$ui)+ process$invoke() |
||
| 49 | +167 |
- )+ }) |
||
| 50 | +168 |
- )+ |
||
| 51 | -+ | |||
| 169 | +1x |
- }+ logger::log_debug("Lockfile creation started based on { getwd() }.")
|
||
| 52 | +170 |
- )+ + |
+ ||
| 171 | +1x | +
+ process |
||
| 53 | +172 |
} |
||
| 54 | +173 | |||
| 55 | +174 |
- #' @rdname module_transform_data+ #' @rdname module_teal_lockfile |
||
| 56 | +175 |
- srv_transform_data <- function(id, data, transformers = list(), modules, is_transformer_failed = reactiveValues()) {
+ .renv_snapshot <- function(lockfile_path) {
|
||
| 57 | -76x - | +176 | +1x |
- checkmate::assert_string(id)+ out <- utils::capture.output( |
| 58 | -76x - | +177 | +1x |
- assert_reactive(data)+ res <- renv::snapshot( |
| 59 | -76x - | +178 | +1x |
- checkmate::assert_list(transformers, "teal_transform_module")+ lockfile = lockfile_path, |
| 60 | -76x - | +179 | +1x |
- checkmate::assert_class(modules, "teal_module")+ prompt = FALSE, |
| 61 | -76x - | +180 | +1x |
- labels <- lapply(transformers, function(x) attr(x, "label"))+ force = TRUE, |
| 62 | -76x - | +181 | +1x |
- ids <- get_unique_labels(labels)+ type = renv::settings$snapshot.type() # see the section "Different ways of creating lockfile" above here |
| 63 | -76x - | +|||
| 182 | +
- names(transformers) <- ids+ ) |
|||
| 64 | -76x - | +|||
| 183 | +
- moduleServer(id, function(input, output, session) {
+ ) |
|||
| 65 | -76x - | +|||
| 184 | +
- logger::log_debug("srv_teal_data_modules initializing.")
+
|
|||
| 66 | -76x - | +185 | +1x |
- Reduce(+ list(out = out, res = res) |
| 67 | -76x - | +|||
| 186 | +
- function(previous_result, name) {
+ } |
|||
| 68 | -19x - | +|||
| 187 | +
- srv_teal_data(+ |
|||
| 69 | -19x - | +|||
| 188 | +
- id = name,+ #' @rdname module_teal_lockfile |
|||
| 70 | -19x - | +|||
| 189 | +
- data_module = function(id) transformers[[name]]$server(id, previous_result),+ .is_lockfile_deps_installed <- function() {
|
|||
| 71 | -19x - | +190 | +1x |
- modules = modules,+ requireNamespace("mirai", quietly = TRUE) && requireNamespace("renv", quietly = TRUE)
|
| 72 | -19x - | +|||
| 191 | +
- is_transformer_failed = is_transformer_failed+ } |
|||
| 73 | +192 |
- )+ |
||
| 74 | +193 |
- },+ #' @rdname module_teal_lockfile+ |
+ ||
| 194 | ++ |
+ .is_disabled_lockfile_scenario <- function() {
|
||
| 75 | -76x - | +195 | +79x |
- x = names(transformers),+ identical(Sys.getenv("CALLR_IS_RUNNING"), "true") || # inside callr process
|
| 76 | -76x - | +196 | +79x |
- init = data+ identical(Sys.getenv("TESTTHAT"), "true") || # inside devtools::test
|
| 77 | -+ | |||
| 197 | +79x |
- )+ !identical(Sys.getenv("QUARTO_PROJECT_ROOT"), "") || # inside Quarto process
|
||
| 78 | +198 |
- })+ (+ |
+ ||
| 199 | +79x | +
+ ("CheckExEnv" %in% search()) || any(c("_R_CHECK_TIMINGS_", "_R_CHECK_LICENSE_") %in% names(Sys.getenv()))
+ |
+ ||
| 200 | +79x | +
+ ) # inside R CMD CHECK |
||
| 79 | +201 |
}@@ -34824,64 +32778,56 @@ teal coverage - 59.73% | ||
| 25 | -4x - | +4x |
checkmate::assert_character(src, min.len = 0, max.len = 1) |
|
| 26 | -4x - | +4x |
params <- list(...) |
|
| 27 | -4x - | +4x |
params$eval <- FALSE |
|
| 28 | -4x - | +4x |
rblock <- RcodeBlock$new(src) |
|
| 29 | -4x - | +4x |
rblock$set_params(params) |
|
| 30 | -4x - | +4x |
self$append_content(rblock) |
|
| 31 | -4x - | +4x |
self$append_metadata("SRC", src)
|
|
| 32 | -4x - | +4x |
invisible(self) |
@@ -34951,32 +32897,28 @@ |
| 42 | -5x - | +5x |
checkmate::assert_class(fs, "teal_slices") |
|
| 43 | -4x - | +4x |
self$append_text("Filter State", "header3")
|
|
| 44 | -4x - | +4x |
if (length(fs)) {
|
|
| 45 | -3x - | +3x |
self$append_content(TealSlicesBlock$new(fs)) |
@@ -34990,8 +32932,7 @@ |
| 47 | -1x - | +1x |
self$append_text("No filters specified.")
|
@@ -35005,8 +32946,7 @@ |
| 49 | -4x - | +4x |
invisible(self) |
@@ -35083,64 +33023,56 @@ |
| 60 | -4x - | +4x |
checkmate::assert_list(encodings) |
|
| 61 | -4x - | +4x |
self$append_text("Selected Options", "header3")
|
|
| 62 | -4x - | +4x |
if (requireNamespace("yaml", quietly = TRUE)) {
|
|
| 63 | -4x - | +4x |
self$append_text(yaml::as.yaml(encodings, handlers = list( |
|
| 64 | -4x - | +4x |
POSIXct = function(x) format(x, "%Y-%m-%d"), |
|
| 65 | -4x - | +4x |
POSIXlt = function(x) format(x, "%Y-%m-%d"), |
|
| 66 | -4x - | +4x |
Date = function(x) format(x, "%Y-%m-%d") |
|
| 67 | -4x - | +4x |
)), "verbatim") |
@@ -35168,16 +33100,14 @@ |
| 71 | -4x - | +4x |
self$append_metadata("Encodings", encodings)
|
|
| 72 | -4x - | +4x |
invisible(self) |
@@ -35380,24 +33310,21 @@ |
| 101 | -9x - | +9x |
self$set_content(content) |
|
| 102 | -8x - | +8x |
self$set_style(style) |
|
| 103 | -8x - | +8x |
invisible(self) |
@@ -35488,64 +33415,56 @@ |
| 116 | -9x - | +9x |
checkmate::assert_class(content, "teal_slices") |
|
| 117 | -8x - | +8x |
if (length(content) != 0) {
|
|
| 118 | -6x - | +6x |
states_list <- lapply(content, function(x) {
|
|
| 119 | -6x - | +6x |
x_list <- shiny::isolate(as.list(x)) |
|
| 120 | -6x - | +6x |
if ( |
|
| 121 | -6x - | +6x |
inherits(x_list$choices, c("integer", "numeric", "Date", "POSIXct", "POSIXlt")) &&
|
|
| 122 | -6x - | +6x |
length(x_list$choices) == 2 && |
|
| 123 | -6x - | +6x |
length(x_list$selected) == 2 |
@@ -35580,8 +33499,7 @@ |
| 128 | -6x - | +6x |
if (!is.null(x_list$arg)) {
|
@@ -35609,16 +33527,14 @@ |
| 132 | -6x - | +6x |
x_list <- x_list[ |
|
| 133 | -6x - | +6x |
c("dataname", "varname", "experiment", "arg", "expr", "selected", "range", "keep_na", "keep_inf")
|
@@ -35632,24 +33548,21 @@ |
| 135 | -6x - | +6x |
names(x_list) <- c( |
|
| 136 | -6x - | +6x |
"Dataset name", "Variable name", "Experiment", "Filtering by", "Applied expression", |
|
| 137 | -6x - | +6x |
"Selected Values", "Selected range", "Include NA values", "Include Inf values" |
@@ -35670,8 +33583,7 @@ |
| 140 | -6x - | +6x |
Filter(Negate(is.null), x_list) |
@@ -35692,16 +33604,14 @@ |
| 143 | -6x - | +6x |
if (requireNamespace("yaml", quietly = TRUE)) {
|
|
| 144 | -6x - | +6x |
super$set_content(yaml::as.yaml(states_list)) |
@@ -35736,16 +33646,14 @@ |
| 149 | -8x - | +8x |
private$teal_slices <- content |
|
| 150 | -8x - | +8x |
invisible(self) |
@@ -35843,4236 +33751,4650 @@ |
| 164 | -1x - | +1x |
checkmate::assert_list(x) |
|
| 165 | -1x - | +1x | +
+ checkmate::assert_names(names(x), must.include = c("text", "style"))
+ |
+ |
| 166 | +1x | +
+ super$set_content(x$text)+ |
+ ||
| 167 | +1x | +
+ super$set_style(x$style)+ |
+ ||
| 168 | +1x | +
+ invisible(self)+ |
+ ||
| 169 | ++ |
+ },+ |
+ ||
| 170 | ++ |
+ #' @description Convert the `TealSlicesBlock` to a list.+ |
+ ||
| 171 | ++ |
+ #'+ |
+ ||
| 172 | ++ |
+ #' @return `named list` with a text and style.+ |
+ ||
| 173 | ++ |
+ #' @examples+ |
+ ||
| 174 | ++ |
+ #' TealSlicesBlock <- getFromNamespace("TealSlicesBlock", "teal")
+ |
+ ||
| 175 | ++ |
+ #' block <- TealSlicesBlock$new()+ |
+ ||
| 176 | ++ |
+ #' block$to_list()+ |
+ ||
| 177 | ++ |
+ #'+ |
+ ||
| 178 | ++ |
+ to_list = function() {
+ |
+ ||
| 179 | +2x | +
+ content <- self$get_content()+ |
+ ||
| 180 | +2x | +
+ list(+ |
+ ||
| 181 | +2x | +
+ text = if (length(content)) content else "",+ |
+ ||
| 182 | +2x | +
+ style = self$get_style()+ |
+ ||
| 183 | ++ |
+ )+ |
+ ||
| 184 | ++ |
+ }+ |
+ ||
| 185 | ++ |
+ ),+ |
+ ||
| 186 | ++ |
+ private = list(+ |
+ ||
| 187 | ++ |
+ style = "verbatim",+ |
+ ||
| 188 | ++ |
+ teal_slices = NULL # teal_slices+ |
+ ||
| 189 | ++ |
+ )+ |
+ ||
| 190 | ++ |
+ )+ |
+
| 1 | ++ |
+ #' Filter panel module in teal+ |
+ ||
| 2 | ++ |
+ #'+ |
+ ||
| 3 | ++ |
+ #' Creates filter panel module from `teal_data` object and returns `teal_data`. It is build in a way+ |
+ ||
| 4 | ++ |
+ #' that filter panel changes and anything what happens before (e.g. [`module_init_data`]) is triggering+ |
+ ||
| 5 | ++ |
+ #' further reactive events only if something has changed and if the module is visible. Thanks to+ |
+ ||
| 6 | ++ |
+ #' this special implementation all modules' data are recalculated only for those modules which are+ |
+ ||
| 7 | ++ |
+ #' currently displayed.+ |
+ ||
| 8 | ++ |
+ #'+ |
+ ||
| 9 | ++ |
+ #' @return A `eventReactive` containing `teal_data` containing filtered objects and filter code.+ |
+ ||
| 10 | ++ |
+ #' `eventReactive` triggers only if all conditions are met:+ |
+ ||
| 11 | ++ |
+ #' - tab is selected (`is_active`)+ |
+ ||
| 12 | ++ |
+ #' - when filters are changed (`get_filter_expr` is different than previous)+ |
+ ||
| 13 | ++ |
+ #'+ |
+ ||
| 14 | ++ |
+ #' @inheritParams module_teal_module+ |
+ ||
| 15 | ++ |
+ #' @param active_datanames (`reactive` returning `character`) this module's data names+ |
+ ||
| 16 | ++ |
+ #' @name module_filter_data+ |
+ ||
| 17 | ++ |
+ #' @keywords internal+ |
+ ||
| 18 | ++ |
+ NULL+ |
+ ||
| 19 | ++ | + + | +||
| 20 | ++ |
+ #' @rdname module_filter_data+ |
+ ||
| 21 | ++ |
+ ui_filter_data <- function(id) {
+ |
+ ||
| 22 | +! | +
+ ns <- shiny::NS(id)+ |
+ ||
| 23 | +! | +
+ uiOutput(ns("panel"))
+ |
+ ||
| 24 | ++ |
+ }+ |
+ ||
| 25 | ++ | + + | +||
| 26 | ++ |
+ #' @rdname module_filter_data+ |
+ ||
| 27 | ++ |
+ srv_filter_data <- function(id, datasets, active_datanames, data_rv, is_active) {
+ |
+ ||
| 28 | +79x | +
+ assert_reactive(datasets)+ |
+ ||
| 29 | +79x | +
+ moduleServer(id, function(input, output, session) {
+ |
+ ||
| 30 | +79x | +
+ active_corrected <- reactive(intersect(active_datanames(), datasets()$datanames()))+ |
+ ||
| 31 | +
- checkmate::assert_names(names(x), must.include = c("text", "style"))
+
|
|||
| 166 | -1x - | +32 | +79x |
- super$set_content(x$text)+ output$panel <- renderUI({
|
| 167 | -1x - | +33 | +81x |
- super$set_style(x$style)+ req(inherits(datasets(), "FilteredData")) |
| 168 | -1x - | +34 | +81x |
- invisible(self)+ isolate({
|
| 169 | +35 |
- },+ # render will be triggered only when FilteredData object changes (not when filters change) |
||
| 170 | +36 |
- #' @description Convert the `TealSlicesBlock` to a list.+ # technically it means that teal_data_module needs to be refreshed |
||
| 171 | -+ | |||
| 37 | +81x |
- #'+ logger::log_debug("srv_filter_panel rendering filter panel.")
|
||
| 172 | -+ | |||
| 38 | +81x |
- #' @return `named list` with a text and style.+ if (length(active_corrected())) {
|
||
| 173 | -+ | |||
| 39 | +79x |
- #' @examples+ datasets()$srv_active("filters", active_datanames = active_corrected)
|
||
| 174 | -+ | |||
| 40 | +79x |
- #' TealSlicesBlock <- getFromNamespace("TealSlicesBlock", "teal")
+ datasets()$ui_active(session$ns("filters"), active_datanames = active_corrected)
|
||
| 175 | +41 |
- #' block <- TealSlicesBlock$new()+ } |
||
| 176 | +42 |
- #' block$to_list()+ }) |
||
| 177 | +43 |
- #'+ }) |
||
| 178 | +44 |
- to_list = function() {
+
|
||
| 179 | -2x - | +45 | +79x |
- content <- self$get_content()+ trigger_data <- .observe_active_filter_changed(datasets, is_active, active_corrected, data_rv) |
| 180 | -2x - | +|||
| 46 | +
- list(+ |
|||
| 181 | -2x - | +47 | +79x |
- text = if (length(content)) content else "",+ eventReactive(trigger_data(), {
|
| 182 | -2x - | +48 | +82x |
- style = self$get_style()+ .make_filtered_teal_data(modules, data = data_rv(), datasets = datasets(), datanames = active_corrected()) |
| 183 | +49 |
- )+ }) |
||
| 184 | +50 |
- }+ }) |
||
| 185 | +51 |
- ),+ } |
||
| 186 | +52 |
- private = list(+ |
||
| 187 | +53 |
- style = "verbatim",+ #' @rdname module_filter_data |
||
| 188 | +54 |
- teal_slices = NULL # teal_slices+ .make_filtered_teal_data <- function(modules, data, datasets = NULL, datanames) {
|
||
| 189 | -+ | |||
| 55 | +82x |
- )+ data <- eval_code( |
||
| 190 | -+ | |||
| 56 | +82x |
- )+ data, |
| 1 | -+ | ||
| 57 | +82x |
- #' Send input validation messages to output+ paste0( |
|
| 2 | -+ | ||
| 58 | +82x |
- #'+ ".raw_data <- list2env(list(",
|
|
| 3 | -+ | ||
| 59 | +82x |
- #' Captures messages from `InputValidator` objects and collates them+ toString(sprintf("%1$s = %1$s", sapply(datanames, as.name))),
|
|
| 4 | -+ | ||
| 60 | +82x |
- #' into one message passed to `validate`.+ "))\n", |
|
| 5 | -+ | ||
| 61 | +82x |
- #'+ "lockEnvironment(.raw_data) # @linksto .raw_data" # this is environment and it is shared by qenvs. CAN'T MODIFY! |
|
| 6 | +62 |
- #' `shiny::validate` is used to withhold rendering of an output element until+ ) |
|
| 7 | +63 |
- #' certain conditions are met and to print a validation message in place+ ) |
|
| 8 | -+ | ||
| 64 | +82x |
- #' of the output element.+ filtered_code <- .get_filter_expr(datasets = datasets, datanames = datanames) |
|
| 9 | -+ | ||
| 65 | +82x |
- #' `shinyvalidate::InputValidator` allows to validate input elements+ filtered_teal_data <- .append_evaluated_code(data, filtered_code) |
|
| 10 | -+ | ||
| 66 | +82x |
- #' and to display specific messages in their respective input widgets.+ filtered_datasets <- sapply(datanames, function(x) datasets$get_data(x, filtered = TRUE), simplify = FALSE) |
|
| 11 | -+ | ||
| 67 | +82x |
- #' `validate_inputs` provides a hybrid solution.+ filtered_teal_data <- .append_modified_data(filtered_teal_data, filtered_datasets) |
|
| 12 | -+ | ||
| 68 | +82x |
- #' Given an `InputValidator` object, messages corresponding to inputs that fail validation+ filtered_teal_data |
|
| 13 | +69 |
- #' are extracted and placed in one validation message that is passed to a `validate`/`need` call.+ } |
|
| 14 | +70 |
- #' This way the input `validator` messages are repeated in the output.+ |
|
| 15 | +71 |
- #'+ #' @rdname module_filter_data |
|
| 16 | +72 |
- #' The `...` argument accepts any number of `InputValidator` objects+ .observe_active_filter_changed <- function(datasets, is_active, active_datanames, data_rv) {
|
|
| 17 | -+ | ||
| 73 | +79x |
- #' or a nested list of such objects.+ previous_signature <- reactiveVal(NULL) |
|
| 18 | -+ | ||
| 74 | +79x |
- #' If `validators` are passed directly, all their messages are printed together+ filter_changed <- reactive({
|
|
| 19 | -+ | ||
| 75 | +181x |
- #' under one (optional) header message specified by `header`. If a list is passed,+ req(inherits(datasets(), "FilteredData")) |
|
| 20 | -+ | ||
| 76 | +181x |
- #' messages are grouped by `validator`. The list's names are used as headers+ new_signature <- c( |
|
| 21 | -+ | ||
| 77 | +181x |
- #' for their respective message groups.+ teal.code::get_code(data_rv()), |
|
| 22 | -+ | ||
| 78 | +181x |
- #' If neither of the nested list elements is named, a header message is taken from `header`.+ .get_filter_expr(datasets = datasets(), datanames = active_datanames()) |
|
| 23 | +79 |
- #'+ ) |
|
| 24 | -+ | ||
| 80 | +181x |
- #' @param ... either any number of `InputValidator` objects+ if (!identical(previous_signature(), new_signature)) {
|
|
| 25 | -+ | ||
| 81 | +87x |
- #' or an optionally named, possibly nested `list` of `InputValidator`+ previous_signature(new_signature) |
|
| 26 | -+ | ||
| 82 | +87x |
- #' objects, see `Details`+ TRUE |
|
| 27 | +83 |
- #' @param header (`character(1)`) generic validation message; set to NULL to omit+ } else {
|
|
| 28 | -+ | ||
| 84 | +94x |
- #'+ FALSE |
|
| 29 | +85 |
- #' @return+ } |
|
| 30 | +86 |
- #' Returns NULL if the final validation call passes and a `shiny.silent.error` if it fails.+ }) |
|
| 31 | +87 |
- #'+ |
|
| 32 | -+ | ||
| 88 | +79x |
- #' @seealso [`shinyvalidate::InputValidator`], [`shiny::validate`]+ trigger_data <- reactiveVal(NULL) |
|
| 33 | -+ | ||
| 89 | +79x |
- #'+ observe({
|
|
| 34 | -+ | ||
| 90 | +194x |
- #' @examplesIf require("shinyvalidate")
+ if (isTRUE(is_active() && filter_changed())) {
|
|
| 35 | -+ | ||
| 91 | +87x |
- #' library(shiny)+ isolate({
|
|
| 36 | -+ | ||
| 92 | +87x |
- #' library(shinyvalidate)+ if (is.null(trigger_data())) {
|
|
| 37 | -+ | ||
| 93 | +79x |
- #'+ trigger_data(0) |
|
| 38 | +94 |
- #' ui <- fluidPage(+ } else {
|
|
| 39 | -+ | ||
| 95 | +8x |
- #' selectInput("method", "validation method", c("sequential", "combined", "grouped")),
+ trigger_data(trigger_data() + 1) |
|
| 40 | +96 |
- #' sidebarLayout(+ } |
|
| 41 | +97 |
- #' sidebarPanel(+ }) |
|
| 42 | +98 |
- #' selectInput("letter", "select a letter:", c(letters[1:3], LETTERS[4:6])),
+ } |
|
| 43 | +99 |
- #' selectInput("number", "select a number:", 1:6),
+ }) |
|
| 44 | +100 |
- #' tags$br(),+ |
|
| 45 | -+ | ||
| 101 | +79x |
- #' selectInput("color", "select a color:",
+ trigger_data |
|
| 46 | +102 |
- #' c("black", "indianred2", "springgreen2", "cornflowerblue"),
+ } |
|
| 47 | +103 |
- #' multiple = TRUE+ |
|
| 48 | +104 |
- #' ),+ #' @rdname module_filter_data |
|
| 49 | +105 |
- #' sliderInput("size", "select point size:",
+ .get_filter_expr <- function(datasets, datanames) {
|
|
| 50 | -+ | ||
| 106 | +263x |
- #' min = 0.1, max = 4, value = 0.25+ if (length(datanames)) {
+ |
+ |
| 107 | +257x | +
+ teal.slice::get_filter_expr(datasets = datasets, datanames = datanames) |
|
| 51 | +108 |
- #' )+ } else {
+ |
+ |
| 109 | +6x | +
+ NULL |
|
| 52 | +110 |
- #' ),+ } |
|
| 53 | +111 |
- #' mainPanel(plotOutput("plot"))
+ } |
| 54 | +1 |
- #' )+ # This is the main function from teal to be used by the end-users. Although it delegates |
||
| 55 | +2 |
- #' )+ # directly to `module_teal_with_splash.R`, we keep it in a separate file because its documentation is quite large |
||
| 56 | +3 |
- #'+ # and it is very end-user oriented. It may also perform more argument checking with more informative |
||
| 57 | +4 |
- #' server <- function(input, output) {
+ # error messages. |
||
| 58 | +5 |
- #' # set up input validation+ |
||
| 59 | +6 |
- #' iv <- InputValidator$new()+ #' Create the server and UI function for the `shiny` app |
||
| 60 | +7 |
- #' iv$add_rule("letter", sv_in_set(LETTERS, "choose a capital letter"))
+ #' |
||
| 61 | +8 |
- #' iv$add_rule("number", function(x) {
+ #' @description `r lifecycle::badge("stable")`
|
||
| 62 | +9 |
- #' if (as.integer(x) %% 2L == 1L) "choose an even number"+ #' |
||
| 63 | +10 |
- #' })+ #' End-users: This is the most important function for you to start a |
||
| 64 | +11 |
- #' iv$enable()+ #' `teal` app that is composed of `teal` modules. |
||
| 65 | +12 |
- #' # more input validation+ #' |
||
| 66 | +13 |
- #' iv_par <- InputValidator$new()+ #' @param data (`teal_data` or `teal_data_module`) |
||
| 67 | +14 |
- #' iv_par$add_rule("color", sv_required(message = "choose a color"))
+ #' For constructing the data object, refer to [teal_data()] and [teal_data_module()]. |
||
| 68 | +15 |
- #' iv_par$add_rule("color", function(x) {
+ #' If `datanames` are not set for the `teal_data` object, defaults from the `teal_data` environment will be used. |
||
| 69 | +16 |
- #' if (length(x) > 1L) "choose only one color"+ #' @param modules (`list` or `teal_modules` or `teal_module`) |
||
| 70 | +17 |
- #' })+ #' Nested list of `teal_modules` or `teal_module` objects or a single |
||
| 71 | +18 |
- #' iv_par$add_rule(+ #' `teal_modules` or `teal_module` object. These are the specific output modules which |
||
| 72 | +19 |
- #' "size",+ #' will be displayed in the `teal` application. See [modules()] and [module()] for |
||
| 73 | +20 |
- #' sv_between(+ #' more details. |
||
| 74 | +21 |
- #' left = 0.5, right = 3,+ #' @param filter (`teal_slices`) Optionally, |
||
| 75 | +22 |
- #' message_fmt = "choose a value between {left} and {right}"
+ #' specifies the initial filter using [teal_slices()]. |
||
| 76 | +23 |
- #' )+ #' @param title (`shiny.tag` or `character(1)`) Optionally, |
||
| 77 | +24 |
- #' )+ #' the browser window title. Defaults to a title "teal app" with the icon of NEST. |
||
| 78 | +25 |
- #' iv_par$enable()+ #' Can be created using the `build_app_title()` or |
||
| 79 | +26 |
- #'+ #' by passing a valid `shiny.tag` which is a head tag with title and link tag. |
||
| 80 | +27 |
- #' output$plot <- renderPlot({
+ #' @param header (`shiny.tag` or `character(1)`) Optionally, |
||
| 81 | +28 |
- #' # validate output+ #' the header of the app. |
||
| 82 | +29 |
- #' switch(input[["method"]],+ #' @param footer (`shiny.tag` or `character(1)`) Optionally, |
||
| 83 | +30 |
- #' "sequential" = {
+ #' the footer of the app. |
||
| 84 | +31 |
- #' validate_inputs(iv)+ #' @param id (`character`) Optionally, |
||
| 85 | +32 |
- #' validate_inputs(iv_par, header = "Set proper graphical parameters")+ #' a string specifying the `shiny` module id in cases it is used as a `shiny` module |
||
| 86 | +33 |
- #' },+ #' rather than a standalone `shiny` app. This is a legacy feature. |
||
| 87 | +34 |
- #' "combined" = validate_inputs(iv, iv_par),+ #' @param landing_popup (`teal_module_landing`) Optionally, |
||
| 88 | +35 |
- #' "grouped" = validate_inputs(list(+ #' a `landing_popup_module` to show up as soon as the teal app is initialized. |
||
| 89 | +36 |
- #' "Some inputs require attention" = iv,+ #' |
||
| 90 | +37 |
- #' "Set proper graphical parameters" = iv_par+ #' @return Named list containing server and UI functions. |
||
| 91 | +38 |
- #' ))+ #' |
||
| 92 | +39 |
- #' )+ #' @export |
||
| 93 | +40 |
#' |
||
| 94 | +41 |
- #' plot(faithful$eruptions ~ faithful$waiting,+ #' @include modules.R |
||
| 95 | +42 |
- #' las = 1, pch = 16,+ #' |
||
| 96 | +43 |
- #' col = input[["color"]], cex = input[["size"]]+ #' @examples |
||
| 97 | +44 |
- #' )+ #' app <- init( |
||
| 98 | +45 |
- #' })+ #' data = within( |
||
| 99 | +46 |
- #' }+ #' teal_data(), |
||
| 100 | +47 |
- #'+ #' {
|
||
| 101 | +48 |
- #' if (interactive()) {
+ #' new_iris <- transform(iris, id = seq_len(nrow(iris))) |
||
| 102 | +49 |
- #' shinyApp(ui, server)+ #' new_mtcars <- transform(mtcars, id = seq_len(nrow(mtcars))) |
||
| 103 | +50 |
- #' }+ #' } |
||
| 104 | +51 |
- #'+ #' ), |
||
| 105 | +52 |
- #' @export+ #' modules = modules( |
||
| 106 | +53 |
- #'+ #' module( |
||
| 107 | +54 |
- validate_inputs <- function(..., header = "Some inputs require attention") {
+ #' label = "data source", |
||
| 108 | -36x - | +|||
| 55 | +
- dots <- list(...)+ #' server = function(input, output, session, data) {},
|
|||
| 109 | -2x - | +|||
| 56 | +
- if (!is_validators(dots)) stop("validate_inputs accepts validators or a list thereof")
+ #' ui = function(id, ...) tags$div(p("information about data source")),
|
|||
| 110 | +57 |
-
+ #' datanames = "all" |
||
| 111 | -34x - | +|||
| 58 | +
- messages <- extract_validator(dots, header)+ #' ), |
|||
| 112 | -34x - | +|||
| 59 | +
- failings <- if (!any_names(dots)) {
+ #' example_module(label = "example teal module"), |
|||
| 113 | -29x - | +|||
| 60 | +
- add_header(messages, header)+ #' module( |
|||
| 114 | +61 |
- } else {
+ #' "Iris Sepal.Length histogram", |
||
| 115 | -5x - | +|||
| 62 | +
- unlist(messages)+ #' server = function(input, output, session, data) {
|
|||
| 116 | +63 |
- }+ #' output$hist <- renderPlot( |
||
| 117 | +64 |
-
+ #' hist(data()[["new_iris"]]$Sepal.Length) |
||
| 118 | -34x - | +|||
| 65 | +
- shiny::validate(shiny::need(is.null(failings), failings))+ #' ) |
|||
| 119 | +66 |
- }+ #' }, |
||
| 120 | +67 |
-
+ #' ui = function(id, ...) {
|
||
| 121 | +68 |
- ### internal functions+ #' ns <- NS(id) |
||
| 122 | +69 |
-
+ #' plotOutput(ns("hist"))
|
||
| 123 | +70 |
- #' @noRd+ #' }, |
||
| 124 | +71 |
- #' @keywords internal+ #' datanames = "new_iris" |
||
| 125 | +72 |
- # recursive object type test+ #' ) |
||
| 126 | +73 |
- # returns logical of length 1+ #' ), |
||
| 127 | +74 |
- is_validators <- function(x) {
+ #' filter = teal_slices( |
||
| 128 | -118x - | +|||
| 75 | +
- all(if (is.list(x)) unlist(lapply(x, is_validators)) else inherits(x, "InputValidator"))+ #' teal_slice(dataname = "new_iris", varname = "Species"), |
|||
| 129 | +76 |
- }+ #' teal_slice(dataname = "new_iris", varname = "Sepal.Length"), |
||
| 130 | +77 |
-
+ #' teal_slice(dataname = "new_mtcars", varname = "cyl"), |
||
| 131 | +78 |
- #' @noRd+ #' exclude_varnames = list(new_iris = c("Sepal.Width", "Petal.Width")),
|
||
| 132 | +79 |
- #' @keywords internal+ #' module_specific = TRUE, |
||
| 133 | +80 |
- # test if an InputValidator object is enabled+ #' mapping = list( |
||
| 134 | +81 |
- # returns logical of length 1+ #' `example teal module` = "new_iris Species", |
||
| 135 | +82 |
- # official method requested at https://github.com/rstudio/shinyvalidate/issues/64+ #' `Iris Sepal.Length histogram` = "new_iris Species", |
||
| 136 | +83 |
- validator_enabled <- function(x) {
+ #' global_filters = "new_mtcars cyl" |
||
| 137 | -49x - | +|||
| 84 | +
- x$.__enclos_env__$private$enabled+ #' ) |
|||
| 138 | +85 |
- }+ #' ), |
||
| 139 | +86 |
-
+ #' title = "App title", |
||
| 140 | +87 |
- #' Recursively extract messages from validator list+ #' header = tags$h1("Sample App"),
|
||
| 141 | +88 |
- #' @return A character vector or a list of character vectors, possibly nested and named.+ #' footer = tags$p("Sample footer")
|
||
| 142 | +89 |
- #' @noRd+ #' ) |
||
| 143 | +90 |
- #' @keywords internal+ #' if (interactive()) {
|
||
| 144 | +91 |
- extract_validator <- function(iv, header) {
+ #' shinyApp(app$ui, app$server) |
||
| 145 | -113x - | +|||
| 92 | +
- if (inherits(iv, "InputValidator")) {
+ #' } |
|||
| 146 | -49x - | +|||
| 93 | +
- add_header(gather_messages(iv), header)+ #' |
|||
| 147 | +94 |
- } else {
+ init <- function(data, |
||
| 148 | -58x - | +|||
| 95 | +
- if (is.null(names(iv))) names(iv) <- rep("", length(iv))
+ modules, |
|||
| 149 | -64x - | +|||
| 96 | +
- mapply(extract_validator, iv = iv, header = names(iv), SIMPLIFY = FALSE)+ filter = teal_slices(), |
|||
| 150 | +97 |
- }+ title = build_app_title(), |
||
| 151 | +98 |
- }+ header = tags$p(), |
||
| 152 | +99 |
-
+ footer = tags$p(), |
||
| 153 | +100 |
- #' Collate failing messages from validator.+ id = character(0), |
||
| 154 | +101 |
- #' @return `list`+ landing_popup = NULL) {
+ |
+ ||
| 102 | +12x | +
+ logger::log_debug("init initializing teal app with: data ('{ class(data) }').")
|
||
| 155 | +103 |
- #' @noRd+ |
||
| 156 | +104 |
- #' @keywords internal+ # argument checking (independent) |
||
| 157 | +105 |
- gather_messages <- function(iv) {
+ ## `data` |
||
| 158 | -49x - | +106 | +12x |
- if (validator_enabled(iv)) {
+ if (inherits(data, "TealData")) {
|
| 159 | -46x - | +|||
| 107 | +! |
- status <- iv$validate()+ lifecycle::deprecate_stop( |
||
| 160 | -46x - | +|||
| 108 | +! |
- failing_inputs <- Filter(Negate(is.null), status)+ when = "0.15.0", |
||
| 161 | -46x - | +|||
| 109 | +! |
- unique(lapply(failing_inputs, function(x) x[["message"]]))+ what = "init(data)", |
||
| 162 | -+ | |||
| 110 | +! |
- } else {
+ paste( |
||
| 163 | -3x - | +|||
| 111 | +! |
- warning("Validator is disabled and will be omitted.")
+ "TealData is no longer supported. Use teal_data() instead.", |
||
| 164 | -3x - | +|||
| 112 | +! |
- list()+ "Please follow migration instructions https://github.com/insightsengineering/teal/discussions/988." |
||
| 165 | +113 |
- }+ ) |
||
| 166 | +114 |
- }+ ) |
||
| 167 | +115 |
-
+ } |
||
| 168 | -+ | |||
| 116 | +12x |
- #' Add optional header to failing messages+ checkmate::assert_multi_class(data, c("teal_data", "teal_data_module"))
|
||
| 169 | -+ | |||
| 117 | +12x |
- #' @noRd+ checkmate::assert_class(landing_popup, "teal_module_landing", null.ok = TRUE) |
||
| 170 | +118 |
- #' @keywords internal+ |
||
| 171 | +119 |
- add_header <- function(messages, header = "") {
+ ## `modules` |
||
| 172 | -78x - | +120 | +12x |
- ans <- unlist(messages)+ checkmate::assert( |
| 173 | -78x - | +121 | +12x |
- if (length(ans) != 0L && isTRUE(nchar(header) > 0L)) {
+ .var.name = "modules", |
| 174 | -31x - | +122 | +12x | +
+ checkmate::check_multi_class(modules, c("teal_modules", "teal_module")),
+ |
+
| 123 | +12x | +
+ checkmate::check_list(modules, min.len = 1, any.missing = FALSE, types = c("teal_module", "teal_modules"))
+ |
+ ||
| 124 | ++ |
+ )+ |
+ ||
| 125 | +12x | +
+ if (inherits(modules, "teal_module")) {
+ |
+ ||
| 126 | +1x |
- ans <- c(paste0(header, "\n"), ans, "\n")+ modules <- list(modules) |
||
| 175 | +127 |
} |
||
| 176 | -78x - | +128 | +12x |
- ans+ if (checkmate::test_list(modules, min.len = 1, any.missing = FALSE, types = c("teal_module", "teal_modules"))) {
+ |
+
| 129 | +6x | +
+ modules <- do.call(teal::modules, modules) |
||
| 177 | +130 |
- }+ } |
||
| 178 | +131 | |||
| 179 | +132 |
- #' Recursively check if the object contains a named list+ ## `filter` |
||
| 180 | -+ | |||
| 133 | +12x |
- #' @noRd+ checkmate::assert_class(filter, "teal_slices") |
||
| 181 | +134 |
- #' @keywords internal+ |
||
| 182 | +135 |
- any_names <- function(x) {
+ ## all other arguments |
||
| 183 | -103x - | +136 | +11x |
- any(+ checkmate::assert( |
| 184 | -103x - | +137 | +11x |
- if (is.list(x)) {
+ .var.name = "title", |
| 185 | -58x - | -
- if (!is.null(names(x)) && any(names(x) != "")) TRUE else unlist(lapply(x, any_names))- |
- ||
| 186 | -+ | 138 | +11x |
- } else {
+ checkmate::check_string(title), |
| 187 | -40x - | +139 | +11x |
- FALSE+ checkmate::check_multi_class(title, c("shiny.tag", "shiny.tag.list", "html"))
|
| 188 | +140 |
- }+ ) |
||
| 189 | -+ | |||
| 141 | +11x |
- )+ checkmate::assert( |
||
| 190 | -+ | |||
| 142 | +11x |
- }+ .var.name = "header", |
| 1 | -+ | ||
| 143 | +11x |
- #' Validate that dataset has a minimum number of observations+ checkmate::check_string(header), |
|
| 2 | -+ | ||
| 144 | +11x |
- #'+ checkmate::check_multi_class(header, c("shiny.tag", "shiny.tag.list", "html"))
|
|
| 3 | +145 |
- #' `r lifecycle::badge("stable")`
+ ) |
|
| 4 | -+ | ||
| 146 | +11x |
- #'+ checkmate::assert( |
|
| 5 | -+ | ||
| 147 | +11x |
- #' This function is a wrapper for `shiny::validate`.+ .var.name = "footer", |
|
| 6 | -+ | ||
| 148 | +11x |
- #'+ checkmate::check_string(footer), |
|
| 7 | -+ | ||
| 149 | +11x |
- #' @param x (`data.frame`)+ checkmate::check_multi_class(footer, c("shiny.tag", "shiny.tag.list", "html"))
|
|
| 8 | +150 |
- #' @param min_nrow (`numeric(1)`) Minimum allowed number of rows in `x`.+ ) |
|
| 9 | -+ | ||
| 151 | +11x |
- #' @param complete (`logical(1)`) Flag specifying whether to check only complete cases. Defaults to `FALSE`.+ checkmate::assert_character(id, max.len = 1, any.missing = FALSE) |
|
| 10 | +152 |
- #' @param allow_inf (`logical(1)`) Flag specifying whether to allow infinite values. Defaults to `TRUE`.+ |
|
| 11 | +153 |
- #' @param msg (`character(1)`) Additional message to display alongside the default message.+ # log |
|
| 12 | -+ | ||
| 154 | +11x |
- #'+ teal.logger::log_system_info() |
|
| 13 | +155 |
- #' @export+ |
|
| 14 | +156 |
- #'+ # argument transformations |
|
| 15 | +157 |
- #' @examples+ ## `modules` - landing module |
|
| 16 | -+ | ||
| 158 | +11x |
- #' library(teal)+ landing <- extract_module(modules, "teal_module_landing") |
|
| 17 | -+ | ||
| 159 | +11x |
- #' ui <- fluidPage(+ if (length(landing) == 1L) {
|
|
| 18 | -+ | ||
| 160 | +! |
- #' sliderInput("len", "Max Length of Sepal",
+ landing_popup <- landing[[1L]] |
|
| 19 | -+ | ||
| 161 | +! |
- #' min = 4.3, max = 7.9, value = 5+ modules <- drop_module(modules, "teal_module_landing") |
|
| 20 | -+ | ||
| 162 | +! |
- #' ),+ lifecycle::deprecate_soft( |
|
| 21 | -+ | ||
| 163 | +! |
- #' plotOutput("plot")
+ when = "0.15.3", |
|
| 22 | -+ | ||
| 164 | +! |
- #' )+ what = "landing_popup_module()", |
|
| 23 | -+ | ||
| 165 | +! |
- #'+ details = paste( |
|
| 24 | -+ | ||
| 166 | +! |
- #' server <- function(input, output) {
+ "Pass `landing_popup_module` to the `landing_popup` argument of the `init` ", |
|
| 25 | -+ | ||
| 167 | +! |
- #' output$plot <- renderPlot({
+ "instead of wrapping it into `modules()` and passing to the `modules` argument" |
|
| 26 | +168 |
- #' iris_df <- iris[iris$Sepal.Length <= input$len, ]+ ) |
|
| 27 | +169 |
- #' validate_has_data(+ ) |
|
| 28 | -+ | ||
| 170 | +11x |
- #' iris_df,+ } else if (length(landing) > 1L) {
|
|
| 29 | -+ | ||
| 171 | +! |
- #' min_nrow = 10,+ stop("Only one `landing_popup_module` can be used.")
|
|
| 30 | +172 |
- #' complete = FALSE,+ } |
|
| 31 | +173 |
- #' msg = "Please adjust Max Length of Sepal"+ |
|
| 32 | +174 |
- #' )+ ## `filter` - set app_id attribute unless present (when restoring bookmark) |
|
| 33 | -+ | ||
| 175 | +11x |
- #'+ if (is.null(attr(filter, "app_id", exact = TRUE))) attr(filter, "app_id") <- create_app_id(data, modules) |
|
| 34 | +176 |
- #' hist(iris_df$Sepal.Length, breaks = 5)+ |
|
| 35 | +177 |
- #' })+ ## `filter` - convert teal.slice::teal_slices to teal::teal_slices |
|
| 36 | -+ | ||
| 178 | +11x |
- #' }+ filter <- as.teal_slices(as.list(filter)) |
|
| 37 | +179 |
- #' if (interactive()) {
+
|
|
| 38 | +180 |
- #' shinyApp(ui, server)+ # argument checking (interdependent) |
|
| 39 | +181 |
- #' }+ ## `filter` - `modules` |
|
| 40 | -+ | ||
| 182 | +11x |
- #'+ if (isTRUE(attr(filter, "module_specific"))) {
|
|
| 41 | -+ | ||
| 183 | +! |
- validate_has_data <- function(x,+ module_names <- unlist(c(module_labels(modules), "global_filters")) |
|
| 42 | -+ | ||
| 184 | +! |
- min_nrow = NULL,+ failed_mod_names <- setdiff(names(attr(filter, "mapping")), module_names) |
|
| 43 | -+ | ||
| 185 | +! |
- complete = FALSE,+ if (length(failed_mod_names)) {
|
|
| 44 | -+ | ||
| 186 | +! |
- allow_inf = TRUE,+ stop( |
|
| 45 | -+ | ||
| 187 | +! |
- msg = NULL) {
+ sprintf( |
|
| 46 | -17x - | +||
| 188 | +! |
- checkmate::assert_string(msg, null.ok = TRUE)+ "Some module names in the mapping arguments don't match module labels.\n %s not in %s", |
|
| 47 | -15x - | +||
| 189 | +! |
- checkmate::assert_data_frame(x)+ toString(failed_mod_names), |
|
| 48 | -15x - | +||
| 190 | +! |
- if (!is.null(min_nrow)) {
+ toString(unique(module_names)) |
|
| 49 | -15x - | +||
| 191 | +
- if (complete) {
+ ) |
||
| 50 | -5x - | +||
| 192 | +
- complete_index <- stats::complete.cases(x)+ ) |
||
| 51 | -5x - | +||
| 193 | +
- validate(need(+ } |
||
| 52 | -5x - | +||
| 194 | +
- sum(complete_index) > 0 && nrow(x[complete_index, , drop = FALSE]) >= min_nrow,+ |
||
| 53 | -5x - | +||
| 195 | +! |
- paste(c(paste("Number of complete cases is less than:", min_nrow), msg), collapse = "\n")
+ if (anyDuplicated(module_names)) {
|
|
| 54 | +196 |
- ))+ # In teal we are able to set nested modules with duplicated label. |
|
| 55 | +197 |
- } else {
+ # Because mapping argument bases on the relationship between module-label and filter-id, |
|
| 56 | -10x - | +||
| 198 | +
- validate(need(+ # it is possible that module-label in mapping might refer to multiple teal_module (identified by the same label) |
||
| 57 | -10x - | +||
| 199 | +! |
- nrow(x) >= min_nrow,+ stop( |
|
| 58 | -10x - | +||
| 200 | +! |
- paste(+ sprintf( |
|
| 59 | -10x - | +||
| 201 | +! |
- c(paste("Minimum number of records not met: >=", min_nrow, "records required."), msg),
+ "Module labels should be unique when teal_slices(mapping = TRUE). Duplicated labels:\n%s ", |
|
| 60 | -10x - | +||
| 202 | +! |
- collapse = "\n"+ toString(module_names[duplicated(module_names)]) |
|
| 61 | +203 |
) |
|
| 62 | +204 |
- ))+ ) |
|
| 63 | +205 |
} |
|
| 64 | +206 | - - | -|
| 65 | -10x - | -
- if (!allow_inf) {
- |
- |
| 66 | -6x - | -
- validate(need(- |
- |
| 67 | -6x - | -
- all(vapply(x, function(col) !is.numeric(col) || !any(is.infinite(col)), logical(1))),- |
- |
| 68 | -6x - | -
- "Dataframe contains Inf values which is not allowed."+ } |
|
| 69 | +207 |
- ))+ |
|
| 70 | +208 |
- }- |
- |
| 71 | -+ | ||
| 209 | +11x |
- }+ if (inherits(data, "teal_data")) {
|
|
| 72 | -+ | ||
| 210 | +10x |
- }+ if (length(ls(teal.code::get_env(data))) == 0) {
|
|
| 73 | -+ | ||
| 211 | +1x |
-
+ stop("The environment of `data` is empty.")
|
|
| 74 | +212 |
- #' Validate that dataset has unique rows for key variables+ } |
|
| 75 | +213 |
- #'+ |
|
| 76 | -+ | ||
| 214 | +9x |
- #' `r lifecycle::badge("stable")`
+ is_modules_ok <- check_modules_datanames(modules, ls(teal.code::get_env(data))) |
|
| 77 | -+ | ||
| 215 | +9x |
- #'+ if (!isTRUE(is_modules_ok) && length(unlist(extract_transformers(modules))) == 0) {
|
|
| 78 | -+ | ||
| 216 | +2x |
- #' This function is a wrapper for `shiny::validate`.+ warning(is_modules_ok, call. = FALSE) |
|
| 79 | +217 |
- #'+ } |
|
| 80 | +218 |
- #' @param x (`data.frame`)+ |
|
| 81 | -+ | ||
| 219 | +9x |
- #' @param key (`character`) Vector of ID variables from `x` that identify unique records.+ is_filter_ok <- check_filter_datanames(filter, ls(teal.code::get_env(data))) |
|
| 82 | -+ | ||
| 220 | +9x |
- #'+ if (!isTRUE(is_filter_ok)) {
|
|
| 83 | -+ | ||
| 221 | +1x |
- #' @export+ warning(is_filter_ok) |
|
| 84 | +222 |
- #'+ # we allow app to continue if applied filters are outside |
|
| 85 | +223 |
- #' @examples+ # of possible data range |
|
| 86 | +224 |
- #' iris$id <- rep(1:50, times = 3)+ } |
|
| 87 | +225 |
- #' ui <- fluidPage(+ } |
|
| 88 | +226 |
- #' selectInput(+ |
|
| 89 | -+ | ||
| 227 | +10x |
- #' inputId = "species",+ reporter <- teal.reporter::Reporter$new()$set_id(attr(filter, "app_id")) |
|
| 90 | -+ | ||
| 228 | +10x |
- #' label = "Select species",+ if (is_arg_used(modules, "reporter") && length(extract_module(modules, "teal_module_previewer")) == 0) {
|
|
| 91 | -+ | ||
| 229 | +! |
- #' choices = c("setosa", "versicolor", "virginica"),
+ modules <- append_module( |
|
| 92 | -+ | ||
| 230 | +! |
- #' selected = "setosa",+ modules, |
|
| 93 | -+ | ||
| 231 | +! |
- #' multiple = TRUE+ reporter_previewer_module(server_args = list(previewer_buttons = c("download", "reset")))
|
|
| 94 | +232 |
- #' ),+ ) |
|
| 95 | +233 |
- #' plotOutput("plot")
+ } |
|
| 96 | +234 |
- #' )+ |
|
| 97 | -+ | ||
| 235 | +10x |
- #' server <- function(input, output) {
+ ns <- NS(id) |
|
| 98 | +236 |
- #' output$plot <- renderPlot({
+ # Note: UI must be a function to support bookmarking. |
|
| 99 | -+ | ||
| 237 | +10x |
- #' iris_f <- iris[iris$Species %in% input$species, ]+ res <- list( |
|
| 100 | -+ | ||
| 238 | +10x |
- #' validate_one_row_per_id(iris_f, key = c("id"))
+ ui = function(request) {
|
|
| 101 | -+ | ||
| 239 | +! |
- #'+ ui_teal( |
|
| 102 | -+ | ||
| 240 | +! |
- #' hist(iris_f$Sepal.Length, breaks = 5)+ id = ns("teal"),
|
|
| 103 | -+ | ||
| 241 | +! |
- #' })+ modules = modules, |
|
| 104 | -+ | ||
| 242 | +! |
- #' }+ title = title, |
|
| 105 | -+ | ||
| 243 | +! |
- #' if (interactive()) {
+ header = header, |
|
| 106 | -+ | ||
| 244 | +! |
- #' shinyApp(ui, server)+ footer = footer |
|
| 107 | +245 |
- #' }+ ) |
|
| 108 | +246 |
- #'+ }, |
|
| 109 | -+ | ||
| 247 | +10x |
- validate_one_row_per_id <- function(x, key = c("USUBJID", "STUDYID")) {
+ server = function(input, output, session) {
|
|
| 110 | +248 | ! |
- validate(need(!any(duplicated(x[key])), paste("Found more than one row per id.")))
+ if (!is.null(landing_popup)) {
|
| 111 | -+ | ||
| 249 | +! |
- }+ do.call(landing_popup$server, c(list(id = "landing_module_shiny_id"), landing_popup$server_args)) |
|
| 112 | +250 |
-
+ } |
|
| 113 | -+ | ||
| 251 | +! |
- #' Validates that vector includes all expected values+ srv_teal(id = ns("teal"), data = data, modules = modules, filter = deep_copy_filter(filter))
|
|
| 114 | +252 |
- #'+ } |
|
| 115 | +253 |
- #' `r lifecycle::badge("stable")`
+ ) |
|
| 116 | +254 |
- #'+ |
|
| 117 | -+ | ||
| 255 | +10x |
- #' This function is a wrapper for `shiny::validate`.+ logger::log_debug("init teal app has been initialized.")
|
|
| 118 | +256 |
- #'+ |
|
| 119 | -+ | ||
| 257 | +10x |
- #' @param x Vector of values to test.+ res |
|
| 120 | +258 |
- #' @param choices Vector to test against.+ } |
| 121 | +1 |
- #' @param msg (`character(1)`) Error message to display if some elements of `x` are not elements of `choices`.+ #' Data module for `teal` applications |
|
| 122 | +2 |
#' |
|
| 123 | +3 |
- #' @export+ #' @description |
|
| 124 | +4 |
- #'+ #' `r lifecycle::badge("experimental")`
|
|
| 125 | +5 |
- #' @examples+ #' |
|
| 126 | +6 |
- #' ui <- fluidPage(+ #' Create a `teal_data_module` object and evaluate code on it with history tracking. |
|
| 127 | +7 |
- #' selectInput(+ #' |
|
| 128 | +8 |
- #' "species",+ #' @details |
|
| 129 | +9 |
- #' "Select species",+ #' `teal_data_module` creates a `shiny` module to interactively supply or modify data in a `teal` application. |
|
| 130 | +10 |
- #' choices = c("setosa", "versicolor", "virginica", "unknown species"),
+ #' The module allows for running any code (creation _and_ some modification) after the app starts or reloads. |
|
| 131 | +11 |
- #' selected = "setosa",+ #' The body of the server function will be run in the app rather than in the global environment. |
|
| 132 | +12 |
- #' multiple = FALSE+ #' This means it will be run every time the app starts, so use sparingly. |
|
| 133 | +13 |
- #' ),+ #' |
|
| 134 | +14 |
- #' verbatimTextOutput("summary")
+ #' Pass this module instead of a `teal_data` object in a call to [init()]. |
|
| 135 | +15 |
- #' )+ #' Note that the server function must always return a `teal_data` object wrapped in a reactive expression. |
|
| 136 | +16 |
#' |
|
| 137 | +17 |
- #' server <- function(input, output) {
+ #' See vignette `vignette("data-as-shiny-module", package = "teal")` for more details.
|
|
| 138 | +18 |
- #' output$summary <- renderPrint({
+ #' |
|
| 139 | +19 |
- #' validate_in(input$species, iris$Species, "Species does not exist.")+ #' @param ui (`function(id)`) |
|
| 140 | +20 |
- #' nrow(iris[iris$Species == input$species, ])+ #' `shiny` module UI function; must only take `id` argument |
|
| 141 | +21 |
- #' })+ #' @param server (`function(id)`) |
|
| 142 | +22 |
- #' }+ #' `shiny` module server function; must only take `id` argument; |
|
| 143 | +23 |
- #' if (interactive()) {
+ #' must return reactive expression containing `teal_data` object |
|
| 144 | +24 |
- #' shinyApp(ui, server)+ #' @param label (`character(1)`) Label of the module. |
|
| 145 | +25 |
- #' }+ #' @param once (`logical(1)`) |
|
| 146 | +26 |
- #'+ #' If `TRUE`, the data module will be shown only once and will disappear after successful data loading. |
|
| 147 | +27 |
- validate_in <- function(x, choices, msg) {
+ #' App user will no longer be able to interact with this module anymore. |
|
| 148 | -! | +||
| 28 | +
- validate(need(length(x) > 0 && length(choices) > 0 && all(x %in% choices), msg))+ #' If `FALSE`, the data module can be reused multiple times. |
||
| 149 | +29 |
- }+ #' App user will be able to interact and change the data output from the module multiple times. |
|
| 150 | +30 |
-
+ #' |
|
| 151 | +31 |
- #' Validates that vector has length greater than 0+ #' @return |
|
| 152 | +32 |
- #'+ #' `teal_data_module` returns a list of class `teal_data_module` containing two elements, `ui` and |
|
| 153 | +33 |
- #' `r lifecycle::badge("stable")`
+ #' `server` provided via arguments. |
|
| 154 | +34 |
#' |
|
| 155 | +35 |
- #' This function is a wrapper for `shiny::validate`.+ #' @examples |
|
| 156 | +36 |
- #'+ #' tdm <- teal_data_module( |
|
| 157 | +37 |
- #' @param x vector+ #' ui = function(id) {
|
|
| 158 | +38 |
- #' @param msg message to display+ #' ns <- NS(id) |
|
| 159 | +39 |
- #'+ #' actionButton(ns("submit"), label = "Load data")
|
|
| 160 | +40 |
- #' @export+ #' }, |
|
| 161 | +41 |
- #'+ #' server = function(id) {
|
|
| 162 | +42 |
- #' @examples+ #' moduleServer(id, function(input, output, session) {
|
|
| 163 | +43 |
- #' data <- data.frame(+ #' eventReactive(input$submit, {
|
|
| 164 | +44 |
- #' id = c(1:10, 11:20, 1:10),+ #' data <- within( |
|
| 165 | +45 |
- #' strata = rep(c("A", "B"), each = 15)
+ #' teal_data(), |
|
| 166 | +46 |
- #' )+ #' {
|
|
| 167 | +47 |
- #' ui <- fluidPage(+ #' dataset1 <- iris |
|
| 168 | +48 |
- #' selectInput("ref1", "Select strata1 to compare",
+ #' dataset2 <- mtcars |
|
| 169 | +49 |
- #' choices = c("A", "B", "C"), selected = "A"
+ #' } |
|
| 170 | +50 |
- #' ),+ #' ) |
|
| 171 | +51 |
- #' selectInput("ref2", "Select strata2 to compare",
+ #' datanames(data) <- c("dataset1", "dataset2")
|
|
| 172 | +52 |
- #' choices = c("A", "B", "C"), selected = "B"
+ #' |
|
| 173 | +53 |
- #' ),+ #' data |
|
| 174 | +54 |
- #' verbatimTextOutput("arm_summary")
+ #' }) |
|
| 175 | +55 |
- #' )+ #' }) |
|
| 176 | +56 |
- #'+ #' } |
|
| 177 | +57 |
- #' server <- function(input, output) {
+ #' ) |
|
| 178 | +58 |
- #' output$arm_summary <- renderText({
+ #' |
|
| 179 | +59 |
- #' sample_1 <- data$id[data$strata == input$ref1]+ #' @name teal_data_module |
|
| 180 | +60 |
- #' sample_2 <- data$id[data$strata == input$ref2]+ #' @seealso [`teal.data::teal_data-class`], [teal.code::qenv()] |
|
| 181 | +61 |
#' |
|
| 182 | +62 |
- #' validate_has_elements(sample_1, "No subjects in strata1.")+ #' @export |
|
| 183 | +63 |
- #' validate_has_elements(sample_2, "No subjects in strata2.")+ teal_data_module <- function(ui, server, label = "data module", once = TRUE) {
|
|
| 184 | -+ | ||
| 64 | +33x |
- #'+ checkmate::assert_function(ui, args = "id", nargs = 1) |
|
| 185 | -+ | ||
| 65 | +32x |
- #' paste0(+ checkmate::assert_function(server, args = "id", nargs = 1) |
|
| 186 | -+ | ||
| 66 | +30x |
- #' "Number of samples in: strata1=", length(sample_1),+ checkmate::assert_string(label) |
|
| 187 | -+ | ||
| 67 | +30x |
- #' " comparions strata2=", length(sample_2)+ checkmate::assert_flag(once) |
|
| 188 | -+ | ||
| 68 | +30x |
- #' )+ structure( |
|
| 189 | -+ | ||
| 69 | +30x |
- #' })+ list( |
|
| 190 | -+ | ||
| 70 | +30x |
- #' }+ ui = ui, |
|
| 191 | -+ | ||
| 71 | +30x |
- #' if (interactive()) {
+ server = function(id) {
|
|
| 192 | -+ | ||
| 72 | +23x |
- #' shinyApp(ui, server)+ data_out <- server(id) |
|
| 193 | -+ | ||
| 73 | +22x |
- #' }+ decorate_err_msg( |
|
| 194 | -+ | ||
| 74 | +22x |
- validate_has_elements <- function(x, msg) {
+ assert_reactive(data_out), |
|
| 195 | -! | +||
| 75 | +22x |
- validate(need(length(x) > 0, msg))+ pre = sprintf("From: 'teal_data_module()':\nA 'teal_data_module' with \"%s\" label:", label),
|
|
| 196 | -+ | ||
| 76 | +22x |
- }+ post = "Please make sure that this module returns a 'reactive` object containing 'teal_data' class of object." # nolint: line_length_linter. |
|
| 197 | +77 |
-
+ ) |
|
| 198 | +78 |
- #' Validates no intersection between two vectors+ } |
|
| 199 | +79 |
- #'+ ), |
|
| 200 | -+ | ||
| 80 | +30x |
- #' `r lifecycle::badge("stable")`
+ label = label, |
|
| 201 | -+ | ||
| 81 | +30x |
- #'+ class = "teal_data_module", |
|
| 202 | -+ | ||
| 82 | +30x |
- #' This function is a wrapper for `shiny::validate`.+ once = once |
|
| 203 | +83 |
- #'+ ) |
|
| 204 | +84 |
- #' @param x vector+ } |
|
| 205 | +85 |
- #' @param y vector+ |
|
| 206 | +86 |
- #' @param msg (`character(1)`) message to display if `x` and `y` intersect+ #' Data module for `teal` transformers. |
|
| 207 | +87 |
#' |
|
| 208 | +88 |
- #' @export+ #' @description |
|
| 209 | +89 |
- #'+ #' `r lifecycle::badge("experimental")`
|
|
| 210 | +90 |
- #' @examples+ #' |
|
| 211 | +91 |
- #' data <- data.frame(+ #' Create a `teal_data_module` object for custom transformation of data for pre-processing |
|
| 212 | +92 |
- #' id = c(1:10, 11:20, 1:10),+ #' before passing the data into the module. |
|
| 213 | +93 |
- #' strata = rep(c("A", "B", "C"), each = 10)
+ #' |
|
| 214 | +94 |
- #' )+ #' @details |
|
| 215 | +95 |
- #'+ #' `teal_transform_module` creates a [`teal_data_module`] object to transform data in a `teal` |
|
| 216 | +96 |
- #' ui <- fluidPage(+ #' application. This transformation happens after the data has passed through the filtering activity |
|
| 217 | +97 |
- #' selectInput("ref1", "Select strata1 to compare",
+ #' in teal. The transformed data is then sent to the server of the [teal_module()]. |
|
| 218 | +98 |
- #' choices = c("A", "B", "C"),
+ #' |
|
| 219 | +99 |
- #' selected = "A"+ #' See vignette `vignette("data-transform-as-shiny-module", package = "teal")` for more details.
|
|
| 220 | +100 |
- #' ),+ #' |
|
| 221 | +101 |
- #' selectInput("ref2", "Select strata2 to compare",
+ #' |
|
| 222 | +102 |
- #' choices = c("A", "B", "C"),
+ #' @inheritParams teal_data_module |
|
| 223 | +103 |
- #' selected = "B"+ #' @param server (`function(id, data)`) |
|
| 224 | +104 |
- #' ),+ #' `shiny` module server function; that takes `id` and `data` argument, |
|
| 225 | +105 |
- #' verbatimTextOutput("summary")
+ #' where the `id` is the module id and `data` is the reactive `teal_data` input. |
|
| 226 | +106 |
- #' )+ #' The server function must return reactive expression containing `teal_data` object. |
|
| 227 | +107 |
#' |
|
| 228 | +108 |
- #' server <- function(input, output) {
+ #' The server function definition should not use `eventReactive` as it may lead to |
|
| 229 | +109 |
- #' output$summary <- renderText({
+ #' unexpected behavior. |
|
| 230 | +110 |
- #' sample_1 <- data$id[data$strata == input$ref1]+ #' See `vignettes("data-transform-as-shiny-module")` for more information.
|
|
| 231 | +111 |
- #' sample_2 <- data$id[data$strata == input$ref2]+ #' @param datanames (`character`) |
|
| 232 | +112 |
- #'+ #' Names of the datasets that are relevant for this module to evaluate. If set to `character(0)` |
|
| 233 | +113 |
- #' validate_no_intersection(+ #' then module would receive [modules()] `datanames`. |
|
| 234 | +114 |
- #' sample_1, sample_2,+ #' @examples |
|
| 235 | +115 |
- #' "subjects within strata1 and strata2 cannot overlap"+ #' my_transformers <- list( |
|
| 236 | +116 |
- #' )+ #' teal_transform_module( |
|
| 237 | +117 |
- #' paste0(+ #' label = "Custom transform for iris", |
|
| 238 | +118 |
- #' "Number of subject in: reference treatment=", length(sample_1),+ #' datanames = "iris", |
|
| 239 | +119 |
- #' " comparions treatment=", length(sample_2)+ #' ui = function(id) {
|
|
| 240 | +120 |
- #' )+ #' ns <- NS(id) |
|
| 241 | +121 |
- #' })+ #' tags$div( |
|
| 242 | +122 |
- #' }+ #' numericInput(ns("n_rows"), "Subset n rows", value = 6, min = 1, max = 150, step = 1)
|
|
| 243 | +123 |
- #' if (interactive()) {
+ #' ) |
|
| 244 | +124 |
- #' shinyApp(ui, server)+ #' }, |
|
| 245 | +125 |
- #' }+ #' server = function(id, data) {
|
|
| 246 | +126 |
- #'+ #' moduleServer(id, function(input, output, session) {
|
|
| 247 | +127 |
- validate_no_intersection <- function(x, y, msg) {
+ #' reactive({
|
|
| 248 | -! | +||
| 128 | +
- validate(need(length(intersect(x, y)) == 0, msg))+ #' within(data(), |
||
| 249 | +129 |
- }+ #' {
|
|
| 250 | +130 |
-
+ #' iris <- head(iris, num_rows) |
|
| 251 | +131 |
-
+ #' }, |
|
| 252 | +132 |
- #' Validates that dataset contains specific variable+ #' num_rows = input$n_rows |
|
| 253 | +133 |
- #'+ #' ) |
|
| 254 | +134 |
- #' `r lifecycle::badge("stable")`
+ #' }) |
|
| 255 | +135 |
- #'+ #' }) |
|
| 256 | +136 |
- #' This function is a wrapper for `shiny::validate`.+ #' } |
|
| 257 | +137 |
- #'+ #' ) |
|
| 258 | +138 |
- #' @param data (`data.frame`)+ #' ) |
|
| 259 | +139 |
- #' @param varname (`character(1)`) name of variable to check for in `data`+ #' |
|
| 260 | +140 |
- #' @param msg (`character(1)`) message to display if `data` does not include `varname`+ #' @name teal_transform_module |
|
| 261 | +141 |
#' |
|
| 262 | +142 |
#' @export |
|
| 263 | +143 |
- #'+ teal_transform_module <- function(ui = function(id) NULL, |
|
| 264 | +144 |
- #' @examples+ server = function(id, data) data, |
|
| 265 | +145 |
- #' data <- data.frame(+ label = "transform module", |
|
| 266 | +146 |
- #' one = rep("a", length.out = 20),
+ datanames = character(0)) {
|
|
| 267 | -+ | ||
| 147 | +19x |
- #' two = rep(c("a", "b"), length.out = 20)
+ checkmate::assert_function(ui, args = "id", nargs = 1) |
|
| 268 | -+ | ||
| 148 | +19x |
- #' )+ checkmate::assert_function(server, args = c("id", "data"), nargs = 2)
|
|
| 269 | -+ | ||
| 149 | +19x |
- #' ui <- fluidPage(+ checkmate::assert_string(label) |
|
| 270 | -+ | ||
| 150 | +19x |
- #' selectInput(+ checkmate::assert_character(datanames) |
|
| 271 | -+ | ||
| 151 | +19x |
- #' "var",+ if (identical(datanames, "all")) {
|
|
| 272 | -+ | ||
| 152 | +1x |
- #' "Select variable",+ stop( |
|
| 273 | -+ | ||
| 153 | +1x |
- #' choices = c("one", "two", "three", "four"),
+ "teal_transform_module can't have datanames property equal to 'all'. Set `datanames = character(0)` instead.", |
|
| 274 | -+ | ||
| 154 | +1x |
- #' selected = "one"+ call. = FALSE |
|
| 275 | +155 |
- #' ),+ ) |
|
| 276 | +156 |
- #' verbatimTextOutput("summary")
+ } |
|
| 277 | -+ | ||
| 157 | +18x |
- #' )+ structure( |
|
| 278 | -+ | ||
| 158 | +18x |
- #'+ list( |
|
| 279 | -+ | ||
| 159 | +18x |
- #' server <- function(input, output) {
+ ui = ui, |
|
| 280 | -+ | ||
| 160 | +18x |
- #' output$summary <- renderText({
+ server = function(id, data) {
|
|
| 281 | -+ | ||
| 161 | +19x |
- #' validate_has_variable(data, input$var)+ data_out <- server(id, data) |
|
| 282 | +162 |
- #' paste0("Selected treatment variables: ", paste(input$var, collapse = ", "))
+
|
|
| 283 | -+ | ||
| 163 | +19x |
- #' })+ if (inherits(data_out, "reactive.event")) {
|
|
| 284 | +164 |
- #' }+ # This warning message partially detects when `eventReactive` is used in `data_module`. |
|
| 285 | -+ | ||
| 165 | +1x |
- #' if (interactive()) {
+ warning( |
|
| 286 | -+ | ||
| 166 | +1x |
- #' shinyApp(ui, server)+ "teal_transform_module() ", |
|
| 287 | -+ | ||
| 167 | +1x |
- #' }+ "Using eventReactive in teal_transform module server code should be avoided as it ", |
|
| 288 | -+ | ||
| 168 | +1x |
- validate_has_variable <- function(data, varname, msg) {
+ "may lead to unexpected behavior. See the vignettes for more information ", |
|
| 289 | -! | +||
| 169 | +1x |
- if (length(varname) != 0) {
+ "(`vignette(\"data-transform-as-shiny-module\", package = \"teal\")`).", |
|
| 290 | -! | +||
| 170 | +1x |
- has_vars <- varname %in% names(data)+ call. = FALSE |
|
| 291 | +171 |
-
+ ) |
|
| 292 | -! | +||
| 172 | +
- if (!all(has_vars)) {
+ } |
||
| 293 | -! | +||
| 173 | +
- if (missing(msg)) {
+
|
||
| 294 | -! | +||
| 174 | +19x |
- msg <- sprintf(+ decorate_err_msg( |
|
| 295 | -! | +||
| 175 | +19x |
- "%s does not have the required variables: %s.",+ assert_reactive(data_out), |
|
| 296 | -! | +||
| 176 | +19x |
- deparse(substitute(data)),+ pre = sprintf("From: 'teal_transform_module()':\nA 'teal_transform_module' with \"%s\" label:", label),
|
|
| 297 | -! | +||
| 177 | +19x |
- toString(varname[!has_vars])+ post = "Please make sure that this module returns a 'reactive` object containing 'teal_data' class of object." # nolint: line_length_linter. |
|
| 298 | +178 |
) |
|
| 299 | +179 |
} |
|
| 300 | -! | +||
| 180 | +
- validate(need(FALSE, msg))+ ), |
||
| 301 | -+ | ||
| 181 | +18x |
- }+ label = label,+ |
+ |
| 182 | +18x | +
+ datanames = datanames,+ |
+ |
| 183 | +18x | +
+ class = c("teal_transform_module", "teal_data_module")
|
|
| 302 | +184 |
- }+ ) |
|
| 303 | +185 |
} |
|
| 304 | +186 | ||
| 305 | +187 |
- #' Validate that variables has expected number of levels+ |
|
| 306 | +188 |
- #'+ #' Extract all `transformers` from `modules`. |
|
| 307 | +189 |
- #' `r lifecycle::badge("stable")`
+ #' |
|
| 308 | +190 |
- #'+ #' @param modules `teal_modules` or `teal_module` |
|
| 309 | +191 |
- #' If the number of levels of `x` is less than `min_levels`+ #' @return A list of `teal_transform_module` nested in the same way as input `modules`. |
|
| 310 | +192 |
- #' or greater than `max_levels` the validation will fail.+ #' @keywords internal |
|
| 311 | +193 |
- #' This function is a wrapper for `shiny::validate`.+ extract_transformers <- function(modules) {
|
|
| 312 | -+ | ||
| 194 | +6x |
- #'+ if (inherits(modules, "teal_module")) {
|
|
| 313 | -+ | ||
| 195 | +3x |
- #' @param x variable name. If `x` is not a factor, the unique values+ modules$transformers |
|
| 314 | -+ | ||
| 196 | +3x |
- #' are treated as levels.+ } else if (inherits(modules, "teal_modules")) {
|
|
| 315 | -+ | ||
| 197 | +3x |
- #' @param min_levels cutoff for minimum number of levels of `x`+ lapply(modules$children, extract_transformers) |
|
| 316 | +198 |
- #' @param max_levels cutoff for maximum number of levels of `x`+ } |
|
| 317 | +199 |
- #' @param var_name name of variable being validated for use in+ } |
| 318 | +1 |
- #' validation message+ #' An example `teal` module |
|
| 319 | +2 |
#' |
|
| 320 | +3 |
- #' @export+ #' `r lifecycle::badge("experimental")`
|
|
| 321 | +4 |
- #' @examples+ #' |
|
| 322 | +5 |
- #' data <- data.frame(+ #' @inheritParams teal_modules |
|
| 323 | +6 |
- #' one = rep("a", length.out = 20),
+ #' @return A `teal` module which can be included in the `modules` argument to [init()]. |
|
| 324 | +7 |
- #' two = rep(c("a", "b"), length.out = 20),
+ #' @examples |
|
| 325 | +8 |
- #' three = rep(c("a", "b", "c"), length.out = 20),
+ #' app <- init( |
|
| 326 | +9 |
- #' four = rep(c("a", "b", "c", "d"), length.out = 20),
+ #' data = teal_data(IRIS = iris, MTCARS = mtcars), |
|
| 327 | +10 |
- #' stringsAsFactors = TRUE+ #' modules = example_module() |
|
| 328 | +11 |
#' ) |
|
| 329 | +12 |
- #' ui <- fluidPage(+ #' if (interactive()) {
|
|
| 330 | +13 |
- #' selectInput(+ #' shinyApp(app$ui, app$server) |
|
| 331 | +14 |
- #' "var",+ #' } |
|
| 332 | +15 |
- #' "Select variable",+ #' @export |
|
| 333 | +16 |
- #' choices = c("one", "two", "three", "four"),
+ example_module <- function(label = "example teal module", datanames = "all", transformers = list()) {
|
|
| 334 | -+ | ||
| 17 | +38x |
- #' selected = "one"+ checkmate::assert_string(label) |
|
| 335 | -+ | ||
| 18 | +38x |
- #' ),+ ans <- module( |
|
| 336 | -+ | ||
| 19 | +38x |
- #' verbatimTextOutput("summary")
+ label, |
|
| 337 | -+ | ||
| 20 | +38x |
- #' )+ server = function(id, data) {
|
|
| 338 | -+ | ||
| 21 | +2x |
- #'+ checkmate::assert_class(isolate(data()), "teal_data") |
|
| 339 | -+ | ||
| 22 | +2x |
- #' server <- function(input, output) {
+ moduleServer(id, function(input, output, session) {
|
|
| 340 | -+ | ||
| 23 | +2x |
- #' output$summary <- renderText({
+ datanames_rv <- reactive(ls(teal.code::get_env((req(data()))))) |
|
| 341 | -+ | ||
| 24 | +2x |
- #' validate_n_levels(data[[input$var]], min_levels = 2, max_levels = 15, var_name = input$var)+ observeEvent(datanames_rv(), {
|
|
| 342 | -+ | ||
| 25 | +2x |
- #' paste0(+ selected <- input$dataname |
|
| 343 | -+ | ||
| 26 | +2x |
- #' "Levels of selected treatment variable: ",+ if (identical(selected, "")) {
|
|
| 344 | -+ | ||
| 27 | +! |
- #' paste(levels(data[[input$var]]),+ selected <- restoreInput(session$ns("dataname"), NULL)
|
|
| 345 | -+ | ||
| 28 | +2x |
- #' collapse = ", "+ } else if (isFALSE(selected %in% datanames_rv())) {
|
|
| 346 | -+ | ||
| 29 | +! |
- #' )+ selected <- datanames_rv()[1] |
|
| 347 | +30 |
- #' )+ } |
|
| 348 | -+ | ||
| 31 | +2x |
- #' })+ updateSelectInput( |
|
| 349 | -+ | ||
| 32 | +2x |
- #' }+ session = session, |
|
| 350 | -+ | ||
| 33 | +2x |
- #' if (interactive()) {
+ inputId = "dataname", |
|
| 351 | -+ | ||
| 34 | +2x |
- #' shinyApp(ui, server)+ choices = datanames_rv(),+ |
+ |
| 35 | +2x | +
+ selected = selected |
|
| 352 | +36 |
- #' }+ ) |
|
| 353 | +37 |
- validate_n_levels <- function(x, min_levels = 1, max_levels = 12, var_name) {
+ }) |
|
| 354 | -! | +||
| 38 | +
- x_levels <- if (is.factor(x)) {
+
|
||
| 355 | -! | +||
| 39 | +2x |
- levels(x)+ output$text <- renderPrint({
|
|
| 356 | -+ | ||
| 40 | +2x |
- } else {
+ req(input$dataname) |
|
| 357 | +41 | ! |
- unique(x)+ data()[[input$dataname]] |
| 358 | +42 |
- }+ }) |
|
| 359 | +43 | ||
| 360 | -! | +||
| 44 | +2x |
- if (!is.null(min_levels) && !(is.null(max_levels))) {
+ teal.widgets::verbatim_popup_srv( |
|
| 361 | -! | +||
| 45 | +2x |
- validate(need(+ id = "rcode", |
|
| 362 | -! | +||
| 46 | +2x |
- length(x_levels) >= min_levels && length(x_levels) <= max_levels,+ verbatim_content = reactive(teal.code::get_code(data())), |
|
| 363 | -! | +||
| 47 | +2x |
- sprintf(+ title = "Example Code" |
|
| 364 | -! | +||
| 48 | +
- "%s variable needs minimum %s level(s) and maximum %s level(s).",+ ) |
||
| 365 | -! | +||
| 49 | +
- var_name, min_levels, max_levels+ }) |
||
| 366 | +50 |
- )+ }, |
|
| 367 | -+ | ||
| 51 | +38x |
- ))+ ui = function(id) {
+ |
+ |
| 52 | +! | +
+ ns <- NS(id)+ |
+ |
| 53 | +! | +
+ teal.widgets::standard_layout( |
|
| 368 | +54 | ! |
- } else if (!is.null(min_levels)) {
+ output = verbatimTextOutput(ns("text")),
|
| 369 | +55 | ! |
- validate(need(+ encoding = tags$div( |
| 370 | +56 | ! |
- length(x_levels) >= min_levels,+ selectInput(ns("dataname"), "Choose a dataset", choices = NULL),
|
| 371 | +57 | ! |
- sprintf("%s variable needs minimum %s levels(s)", var_name, min_levels)
+ teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
|
| 372 | +58 |
- ))+ ) |
|
| 373 | -! | +||
| 59 | +
- } else if (!is.null(max_levels)) {
+ ) |
||
| 374 | -! | +||
| 60 | +
- validate(need(+ }, |
||
| 375 | -! | +||
| 61 | +38x |
- length(x_levels) <= max_levels,+ datanames = datanames, |
|
| 376 | -! | +||
| 62 | +38x |
- sprintf("%s variable needs maximum %s level(s)", var_name, max_levels)
+ transformers = transformers |
|
| 377 | +63 |
- ))+ ) |
|
| 378 | -+ | ||
| 64 | +38x |
- }+ attr(ans, "teal_bookmarkable") <- TRUE+ |
+ |
| 65 | +38x | +
+ ans |
|
| 379 | +66 |
}@@ -40081,1444 +38403,1458 @@ teal coverage - 59.73% |
| 1 |
- #' Data module for `teal` applications+ setOldClass("teal_data_module")
|
||
| 2 |
- #'+ |
||
| 3 |
- #' @description+ #' Evaluate code on `teal_data_module` |
||
| 4 |
- #' `r lifecycle::badge("experimental")`
+ #' |
||
| 5 |
- #'+ #' @details |
||
| 6 |
- #' Create a `teal_data_module` object and evaluate code on it with history tracking.+ #' `eval_code` evaluates given code in the environment of the `teal_data` object created by the `teal_data_module`. |
||
| 7 |
- #'+ #' The code is added to the `@code` slot of the `teal_data`. |
||
| 8 |
- #' @details+ #' |
||
| 9 |
- #' `teal_data_module` creates a `shiny` module to interactively supply or modify data in a `teal` application.+ #' @param object (`teal_data_module`) |
||
| 10 |
- #' The module allows for running any code (creation _and_ some modification) after the app starts or reloads.+ #' @inheritParams teal.code::eval_code |
||
| 11 |
- #' The body of the server function will be run in the app rather than in the global environment.+ #' |
||
| 12 |
- #' This means it will be run every time the app starts, so use sparingly.+ #' @return |
||
| 13 |
- #'+ #' `eval_code` returns a `teal_data_module` object with a delayed evaluation of `code` when the module is run. |
||
| 14 |
- #' Pass this module instead of a `teal_data` object in a call to [init()].+ #' |
||
| 15 |
- #' Note that the server function must always return a `teal_data` object wrapped in a reactive expression.+ #' @examples |
||
| 16 |
- #'+ #' eval_code(tdm, "dataset1 <- subset(dataset1, Species == 'virginica')") |
||
| 17 |
- #' See vignette `vignette("data-as-shiny-module", package = "teal")` for more details.
+ #' |
||
| 18 |
- #'+ #' @include teal_data_module.R |
||
| 19 |
- #' @param ui (`function(id)`)+ #' @name eval_code |
||
| 20 |
- #' `shiny` module UI function; must only take `id` argument+ #' @rdname teal_data_module |
||
| 21 |
- #' @param server (`function(id)`)+ #' @aliases eval_code,teal_data_module,character-method |
||
| 22 |
- #' `shiny` module server function; must only take `id` argument;+ #' @aliases eval_code,teal_data_module,language-method |
||
| 23 |
- #' must return reactive expression containing `teal_data` object+ #' @aliases eval_code,teal_data_module,expression-method |
||
| 24 |
- #' @param label (`character(1)`) Label of the module.+ #' |
||
| 25 |
- #' @param once (`logical(1)`)+ #' @importFrom methods setMethod |
||
| 26 |
- #' If `TRUE`, the data module will be shown only once and will disappear after successful data loading.+ #' @importMethodsFrom teal.code eval_code |
||
| 27 |
- #' App user will no longer be able to interact with this module anymore.+ #' |
||
| 28 |
- #' If `FALSE`, the data module can be reused multiple times.+ setMethod("eval_code", signature = c("teal_data_module", "character"), function(object, code) {
|
||
| 29 | -+ | 9x |
- #' App user will be able to interact and change the data output from the module multiple times.+ teal_data_module( |
| 30 | -+ | 9x |
- #'+ ui = function(id) {
|
| 31 | -+ | 1x |
- #' @return+ ns <- NS(id) |
| 32 | -+ | 1x |
- #' `teal_data_module` returns a list of class `teal_data_module` containing two elements, `ui` and+ object$ui(ns("mutate_inner"))
|
| 33 |
- #' `server` provided via arguments.+ }, |
||
| 34 | -+ | 9x |
- #'+ server = function(id) {
|
| 35 | -+ | 7x |
- #' @examples+ moduleServer(id, function(input, output, session) {
|
| 36 | -+ | 7x |
- #' tdm <- teal_data_module(+ teal_data_rv <- object$server("mutate_inner")
|
| 37 | -+ | 6x |
- #' ui = function(id) {
+ td <- eventReactive(teal_data_rv(), |
| 38 |
- #' ns <- NS(id)+ {
|
||
| 39 | -+ | 6x |
- #' actionButton(ns("submit"), label = "Load data")
+ if (inherits(teal_data_rv(), c("teal_data", "qenv.error"))) {
|
| 40 | -+ | 4x |
- #' },+ eval_code(teal_data_rv(), code) |
| 41 |
- #' server = function(id) {
+ } else {
|
||
| 42 | -+ | 2x |
- #' moduleServer(id, function(input, output, session) {
+ teal_data_rv() |
| 43 |
- #' eventReactive(input$submit, {
+ } |
||
| 44 |
- #' data <- within(+ }, |
||
| 45 | -+ | 6x |
- #' teal_data(),+ ignoreNULL = FALSE |
| 46 |
- #' {
+ ) |
||
| 47 | -+ | 6x |
- #' dataset1 <- iris+ td |
| 48 |
- #' dataset2 <- mtcars+ }) |
||
| 49 |
- #' }+ } |
||
| 50 |
- #' )+ ) |
||
| 51 |
- #' datanames(data) <- c("dataset1", "dataset2")
+ }) |
||
| 52 |
- #'+ |
||
| 53 |
- #' data+ 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 | ++ |
+ #' Include `CSS` files from `/inst/css/` package directory to application header+ |
+ |
| 2 |
#' |
||
| 59 | +3 |
- #' @name teal_data_module+ #' `system.file` should not be used to access files in other packages, it does |
|
| 60 | +4 |
- #' @seealso [`teal.data::teal_data-class`], [teal.code::qenv()]+ #' not work with `devtools`. Therefore, we redefine this method in each package |
|
| 61 | +5 | ++ |
+ #' as needed. Thus, we do not export this method.+ |
+
| 6 |
#' |
||
| 62 | +7 |
- #' @export+ #' @param pattern (`character`) pattern of files to be included |
|
| 63 | +8 |
- teal_data_module <- function(ui, server, label = "data module", once = TRUE) {
+ #' |
|
| 64 | -33x - | +||
| 9 | +
- checkmate::assert_function(ui, args = "id", nargs = 1)+ #' @return HTML code that includes `CSS` files. |
||
| 65 | -32x - | +||
| 10 | +
- checkmate::assert_function(server, args = "id", nargs = 1)+ #' @keywords internal |
||
| 66 | -30x - | +||
| 11 | +
- checkmate::assert_string(label)+ include_css_files <- function(pattern = "*") {
|
||
| 67 | -30x - | +||
| 12 | +! |
- checkmate::assert_flag(once)+ css_files <- list.files( |
|
| 68 | -30x - | +||
| 13 | +! |
- structure(+ system.file("css", package = "teal", mustWork = TRUE),
|
|
| 69 | -30x - | +||
| 14 | +! |
- list(+ pattern = pattern, full.names = TRUE |
|
| 70 | -30x - | +||
| 15 | +
- ui = ui,+ ) |
||
| 71 | -30x - | +||
| 16 | +
- server = function(id) {
+
|
||
| 72 | -23x - | +||
| 17 | +! |
- data_out <- server(id)+ singleton( |
|
| 73 | -22x - | +||
| 18 | +! |
- decorate_err_msg(+ tags$head(lapply(css_files, includeCSS)) |
|
| 74 | -22x - | +||
| 19 | +
- assert_reactive(data_out),+ ) |
||
| 75 | -22x - | +||
| 20 | +
- pre = sprintf("From: 'teal_data_module()':\nA 'teal_data_module' with \"%s\" label:", label),
+ } |
||
| 76 | -22x - | +||
| 21 | +
- post = "Please make sure that this module returns a 'reactive` object containing 'teal_data' class of object." # nolint: line_length_linter.+ |
||
| 77 | +22 |
- )+ #' Include `JS` files from `/inst/js/` package directory to application header |
|
| 78 | +23 |
- }+ #' |
|
| 79 | +24 |
- ),+ #' `system.file` should not be used to access files in other packages, it does |
|
| 80 | -30x - | +||
| 25 | +
- label = label,+ #' not work with `devtools`. Therefore, we redefine this method in each package |
||
| 81 | -30x - | +||
| 26 | +
- class = "teal_data_module",+ #' as needed. Thus, we do not export this method |
||
| 82 | -30x - | +||
| 27 | +
- once = once+ #' |
||
| 83 | +28 |
- )+ #' @param pattern (`character`) pattern of files to be included, passed to `system.file` |
|
| 84 | +29 | ++ |
+ #' @param except (`character`) vector of basename filenames to be excluded+ |
+
| 30 | ++ |
+ #'+ |
+ |
| 31 | ++ |
+ #' @return HTML code that includes `JS` files.+ |
+ |
| 32 | ++ |
+ #' @keywords internal+ |
+ |
| 33 | ++ |
+ include_js_files <- function(pattern = NULL, except = NULL) {
+ |
+ |
| 34 | +! | +
+ checkmate::assert_character(except, min.len = 1, any.missing = FALSE, null.ok = TRUE)+ |
+ |
| 35 | +! | +
+ js_files <- list.files(system.file("js", package = "teal", mustWork = TRUE), pattern = pattern, full.names = TRUE)
+ |
+ |
| 36 | +! | +
+ js_files <- js_files[!(basename(js_files) %in% except)] # no-op if except is NULL+ |
+ |
| 37 | ++ | + + | +|
| 38 | +! | +
+ singleton(lapply(js_files, includeScript))+ |
+ |
| 39 |
} |
||
| 85 | +40 | ||
| 86 | +41 |
- #' Data module for `teal` transformers.+ #' Run `JS` file from `/inst/js/` package directory |
|
| 87 | +42 |
#' |
|
| 88 | +43 |
- #' @description+ #' This is triggered from the server to execute on the client+ |
+ |
| 44 | ++ |
+ #' rather than triggered directly on the client.+ |
+ |
| 45 | ++ |
+ #' Unlike `include_js_files` which includes `JavaScript` functions,+ |
+ |
| 46 | ++ |
+ #' the `run_js` actually executes `JavaScript` functions. |
|
| 89 | +47 |
- #' `r lifecycle::badge("experimental")`
+ #' |
|
| 90 | +48 |
- #'+ #' `system.file` should not be used to access files in other packages, it does |
|
| 91 | +49 |
- #' Create a `teal_data_module` object for custom transformation of data for pre-processing+ #' not work with `devtools`. Therefore, we redefine this method in each package |
|
| 92 | +50 |
- #' before passing the data into the module.+ #' as needed. Thus, we do not export this method. |
|
| 93 | +51 |
#' |
|
| 94 | +52 |
- #' @details+ #' @param files (`character`) vector of filenames. |
|
| 95 | +53 |
- #' `teal_transform_module` creates a [`teal_data_module`] object to transform data in a `teal`+ #' |
|
| 96 | +54 |
- #' application. This transformation happens after the data has passed through the filtering activity+ #' @return `NULL`, invisibly. |
|
| 97 | +55 |
- #' in teal. The transformed data is then sent to the server of the [teal_module()].+ #' @keywords internal |
|
| 98 | +56 |
- #'+ run_js_files <- function(files) {
|
|
| 99 | -+ | ||
| 57 | +81x |
- #' See vignette `vignette("data-transform-as-shiny-module", package = "teal")` for more details.
+ checkmate::assert_character(files, min.len = 1, any.missing = FALSE) |
|
| 100 | -+ | ||
| 58 | +81x |
- #'+ lapply(files, function(file) {
|
|
| 101 | -+ | ||
| 59 | +81x |
- #'+ shinyjs::runjs(paste0(readLines(system.file("js", file, package = "teal", mustWork = TRUE)), collapse = "\n"))
|
|
| 102 | +60 |
- #' @inheritParams teal_data_module+ }) |
|
| 103 | -+ | ||
| 61 | +81x |
- #' @param server (`function(id, data)`)+ invisible(NULL) |
|
| 104 | +62 |
- #' `shiny` module server function; that takes `id` and `data` argument,+ } |
|
| 105 | +63 |
- #' where the `id` is the module id and `data` is the reactive `teal_data` input.+ |
|
| 106 | +64 |
- #' The server function must return reactive expression containing `teal_data` object.+ #' Code to include `teal` `CSS` and `JavaScript` files |
|
| 107 | +65 |
#' |
|
| 108 | +66 |
- #' The server function definition should not use `eventReactive` as it may lead to+ #' This is useful when you want to use the same `JavaScript` and `CSS` files that are |
|
| 109 | +67 |
- #' unexpected behavior.+ #' used with the `teal` application. |
|
| 110 | +68 |
- #' See `vignettes("data-transform-as-shiny-module")` for more information.
+ #' This is also useful for running standalone modules in `teal` with the correct |
|
| 111 | +69 |
- #' @param datanames (`character`)+ #' styles. |
|
| 112 | +70 |
- #' Names of the datasets that are relevant for this module to evaluate. If set to `character(0)`+ #' Also initializes `shinyjs` so you can use it. |
|
| 113 | +71 |
- #' then module would receive [modules()] `datanames`.+ #' |
|
| 114 | +72 |
- #' @examples+ #' Simply add `include_teal_css_js()` as one of the UI elements. |
|
| 115 | +73 |
- #' my_transformers <- list(+ #' @return A `shiny.tag.list`. |
|
| 116 | +74 |
- #' teal_transform_module(+ #' @keywords internal |
|
| 117 | +75 |
- #' label = "Custom transform for iris",+ include_teal_css_js <- function() {
|
|
| 118 | -+ | ||
| 76 | +! |
- #' datanames = "iris",+ tagList( |
|
| 119 | -+ | ||
| 77 | +! |
- #' ui = function(id) {
+ shinyjs::useShinyjs(), |
|
| 120 | -+ | ||
| 78 | +! |
- #' ns <- NS(id)+ include_css_files(), |
|
| 121 | +79 |
- #' tags$div(+ # init.js is executed from the server |
|
| 122 | -+ | ||
| 80 | +! |
- #' numericInput(ns("n_rows"), "Subset n rows", value = 6, min = 1, max = 150, step = 1)
+ include_js_files(except = "init.js"), |
|
| 123 | -+ | ||
| 81 | +! |
- #' )+ shinyjs::hidden(icon("fas fa-gear")), # add hidden icon to load font-awesome css for icons
|
|
| 124 | +82 |
- #' },+ ) |
|
| 125 | +83 |
- #' server = function(id, data) {
+ } |
| 126 | +1 |
- #' moduleServer(id, function(input, output, session) {
+ #' `teal_data` utils |
||
| 127 | +2 |
- #' reactive({
+ #' |
||
| 128 | +3 |
- #' within(data(),+ #' In `teal` we need to recreate the `teal_data` object due to two operations: |
||
| 129 | +4 |
- #' {
+ #' - we need to append filter-data code and objects which have been evaluated in `FilteredData` and |
||
| 130 | +5 |
- #' iris <- head(iris, num_rows)+ #' we want to avoid double-evaluation. |
||
| 131 | +6 |
- #' },+ #' - we need to subset `teal_data` to `datanames` used by the module, to shorten obtainable R-code |
||
| 132 | +7 |
- #' num_rows = input$n_rows+ #' |
||
| 133 | +8 |
- #' )+ #' Due to above recreation of `teal_data` object can't be done simply by using public |
||
| 134 | +9 |
- #' })+ #' `teal.code` and `teal.data` methods. |
||
| 135 | +10 |
- #' })+ #' |
||
| 136 | +11 |
- #' }+ #' @param data (`teal_data`) |
||
| 137 | +12 |
- #' )+ #' @param code (`character`) code to append to `data@code` |
||
| 138 | +13 |
- #' )+ #' @param objects (`list`) objects to append to `data@env` |
||
| 139 | +14 |
- #'+ #' @param datanames (`character`) names of the datasets |
||
| 140 | +15 |
- #' @name teal_transform_module+ #' @return modified `teal_data` |
||
| 141 | +16 |
- #'+ #' @keywords internal |
||
| 142 | +17 |
- #' @export+ #' @name teal_data_utilities |
||
| 143 | +18 |
- teal_transform_module <- function(ui = function(id) NULL,+ NULL |
||
| 144 | +19 |
- server = function(id, data) data,+ |
||
| 145 | +20 |
- label = "transform module",+ #' @rdname teal_data_utilities |
||
| 146 | +21 |
- datanames = character(0)) {
- |
- ||
| 147 | -19x - | -
- checkmate::assert_function(ui, args = "id", nargs = 1)+ .append_evaluated_code <- function(data, code) {
|
||
| 148 | -19x - | +22 | +82x |
- checkmate::assert_function(server, args = c("id", "data"), nargs = 2)
+ checkmate::assert_class(data, "teal_data") |
| 149 | -19x - | +23 | +82x |
- checkmate::assert_string(label)+ data@code <- c(data@code, code) |
| 150 | -19x - | +24 | +82x |
- checkmate::assert_character(datanames)+ data@id <- c(data@id, max(data@id) + 1L + seq_along(code)) |
| 151 | -19x - | +25 | +82x |
- if (identical(datanames, "all")) {
+ data@messages <- c(data@messages, rep("", length(code)))
|
| 152 | -1x - | +26 | +82x |
- stop(+ data@warnings <- c(data@warnings, rep("", length(code)))
|
| 153 | -1x - | +27 | +82x |
- "teal_transform_module can't have datanames property equal to 'all'. Set `datanames = character(0)` instead.",+ methods::validObject(data) |
| 154 | -1x - | +28 | +82x |
- call. = FALSE+ data |
| 155 | +29 |
- )+ } |
||
| 156 | +30 |
- }- |
- ||
| 157 | -18x - | -
- structure(- |
- ||
| 158 | -18x - | -
- list(- |
- ||
| 159 | -18x - | -
- ui = ui,- |
- ||
| 160 | -18x - | -
- server = function(id, data) {
- |
- ||
| 161 | -19x - | -
- data_out <- server(id, data)+ |
||
| 162 | +31 | - - | -||
| 163 | -19x - | -
- if (inherits(data_out, "reactive.event")) {
+ #' @rdname teal_data_utilities |
||
| 164 | +32 |
- # This warning message partially detects when `eventReactive` is used in `data_module`.+ .append_modified_data <- function(data, objects) {
|
||
| 165 | -1x - | +33 | +82x |
- warning(+ checkmate::assert_class(data, "teal_data") |
| 166 | -1x - | +34 | +82x |
- "teal_transform_module() ",+ checkmate::assert_class(objects, "list") |
| 167 | -1x - | +35 | +82x |
- "Using eventReactive in teal_transform module server code should be avoided as it ",+ new_env <- list2env(objects, parent = .GlobalEnv) |
| 168 | -1x - | +36 | +82x |
- "may lead to unexpected behavior. See the vignettes for more information ",+ rlang::env_coalesce(new_env, teal.code::get_env(data)) |
| 169 | -1x - | +37 | +82x |
- "(`vignette(\"data-transform-as-shiny-module\", package = \"teal\")`).",+ data@env <- new_env |
| 170 | -1x - | +38 | +82x |
- call. = FALSE+ data |
| 171 | +39 |
- )+ } |
||
| 172 | +40 |
- }+ |
||
| 173 | +41 |
-
+ #' @rdname teal_data_utilities |
||
| 174 | -19x - | +|||
| 42 | +
- decorate_err_msg(+ .subset_teal_data <- function(data, datanames) {
|
|||
| 175 | -19x - | +43 | +81x |
- assert_reactive(data_out),+ checkmate::assert_class(data, "teal_data") |
| 176 | -19x - | +44 | +81x |
- pre = sprintf("From: 'teal_transform_module()':\nA 'teal_transform_module' with \"%s\" label:", label),
+ checkmate::assert_class(datanames, "character") |
| 177 | -19x - | -
- post = "Please make sure that this module returns a 'reactive` object containing 'teal_data' class of object." # nolint: line_length_linter.- |
- ||
| 178 | -- |
- )- |
- ||
| 179 | -- |
- }- |
- ||
| 180 | -+ | 45 | +81x |
- ),+ datanames_corrected <- intersect(datanames, ls(teal.code::get_env(data))) |
| 181 | -18x - | +46 | +81x |
- label = label,+ datanames_corrected_with_raw <- c(datanames_corrected, ".raw_data") |
| 182 | -18x - | +47 | +81x |
- datanames = datanames,+ if (!length(datanames_corrected)) {
|
| 183 | -18x - | +48 | +2x |
- class = c("teal_transform_module", "teal_data_module")
+ return(teal_data()) |
| 184 | +49 |
- )+ } |
||
| 185 | +50 |
- }+ |
||
| 186 | -+ | |||
| 51 | +79x |
-
+ new_data <- do.call( |
||
| 187 | -+ | |||
| 52 | +79x |
-
+ teal.data::teal_data, |
||
| 188 | -+ | |||
| 53 | +79x |
- #' Extract all `transformers` from `modules`.+ args = c( |
||
| 189 | -+ | |||
| 54 | +79x |
- #'+ mget(x = datanames_corrected_with_raw, envir = teal.code::get_env(data)), |
||
| 190 | -+ | |||
| 55 | +79x |
- #' @param modules `teal_modules` or `teal_module`+ list( |
||
| 191 | -+ | |||
| 56 | +79x |
- #' @return A list of `teal_transform_module` nested in the same way as input `modules`.+ code = teal.code::get_code(data, names = datanames_corrected_with_raw), |
||
| 192 | -+ | |||
| 57 | +79x |
- #' @keywords internal+ join_keys = teal.data::join_keys(data)[datanames_corrected] |
||
| 193 | +58 |
- extract_transformers <- function(modules) {
+ ) |
||
| 194 | -4x - | +|||
| 59 | +
- if (inherits(modules, "teal_module")) {
+ ) |
|||
| 195 | -2x - | +|||
| 60 | +
- modules$transformers+ ) |
|||
| 196 | -2x - | +61 | +79x |
- } else if (inherits(modules, "teal_modules")) {
+ new_data@verified <- data@verified |
| 197 | -2x - | +62 | +79x |
- lapply(modules$children, extract_transformers)+ teal.data::datanames(new_data) <- datanames_corrected |
| 198 | -+ | |||
| 63 | +79x |
- }+ new_data |
||
| 199 | +64 |
}@@ -41527,14 +39863,14 @@ teal coverage - 59.73% |
| 1 |
- #' Include `CSS` files from `/inst/css/` package directory to application header+ #' Filter settings for `teal` applications |
||
| 3 |
- #' `system.file` should not be used to access files in other packages, it does+ #' Specify initial filter states and filtering settings for a `teal` app. |
||
| 4 |
- #' not work with `devtools`. Therefore, we redefine this method in each package+ #' |
||
| 5 |
- #' as needed. Thus, we do not export this method.+ #' Produces a `teal_slices` object. |
||
| 6 |
- #'+ #' The `teal_slice` components will specify filter states that will be active when the app starts. |
||
| 7 |
- #' @param pattern (`character`) pattern of files to be included+ #' Attributes (created with the named arguments) will configure the way the app applies filters. |
||
| 8 |
- #'+ #' See argument descriptions for details. |
||
| 9 |
- #' @return HTML code that includes `CSS` files.+ #' |
||
| 10 |
- #' @keywords internal+ #' @inheritParams teal.slice::teal_slices |
||
| 11 |
- include_css_files <- function(pattern = "*") {
+ #' |
||
| 12 | -! | +
- css_files <- list.files(+ #' @param module_specific (`logical(1)`) optional, |
|
| 13 | -! | +
- system.file("css", package = "teal", mustWork = TRUE),
+ #' - `FALSE` (default) when one filter panel applied to all modules. |
|
| 14 | -! | +
- pattern = pattern, full.names = TRUE+ #' All filters will be shared by all modules. |
|
| 15 |
- )+ #' - `TRUE` when filter panel module-specific. |
||
| 16 |
-
+ #' Modules can have different set of filters specified - see `mapping` argument. |
||
| 17 | -! | +
- singleton(+ #' @param mapping `r lifecycle::badge("experimental")`
|
|
| 18 | -! | +
- tags$head(lapply(css_files, includeCSS))+ #' _This is a new feature. Do kindly share your opinions on |
|
| 19 |
- )+ #' [`teal`'s GitHub repository](https://github.com/insightsengineering/teal/)._ |
||
| 20 |
- }+ #' |
||
| 21 |
-
+ #' (named `list`) specifies which filters will be active in which modules on app start. |
||
| 22 |
- #' Include `JS` files from `/inst/js/` package directory to application header+ #' Elements should contain character vector of `teal_slice` `id`s (see [`teal.slice::teal_slice`]). |
||
| 23 |
- #'+ #' Names of the list should correspond to `teal_module` `label` set in [module()] function. |
||
| 24 |
- #' `system.file` should not be used to access files in other packages, it does+ #' - `id`s listed under `"global_filters` will be active in all modules. |
||
| 25 |
- #' not work with `devtools`. Therefore, we redefine this method in each package+ #' - If missing, all filters will be applied to all modules. |
||
| 26 |
- #' as needed. Thus, we do not export this method+ #' - If empty list, all filters will be available to all modules but will start inactive. |
||
| 27 |
- #'+ #' - If `module_specific` is `FALSE`, only `global_filters` will be active on start. |
||
| 28 |
- #' @param pattern (`character`) pattern of files to be included, passed to `system.file`+ #' @param app_id (`character(1)`) |
||
| 29 |
- #' @param except (`character`) vector of basename filenames to be excluded+ #' For internal use only, do not set manually. |
||
| 30 |
- #'+ #' Added by `init` so that a `teal_slices` can be matched to the app in which it was used. |
||
| 31 |
- #' @return HTML code that includes `JS` files.+ #' Used for verifying snapshots uploaded from file. See `snapshot`. |
||
| 32 |
- #' @keywords internal+ #' |
||
| 33 |
- include_js_files <- function(pattern = NULL, except = NULL) {
+ #' @param x (`list`) of lists to convert to `teal_slices` |
||
| 34 | -! | +
- checkmate::assert_character(except, min.len = 1, any.missing = FALSE, null.ok = TRUE)+ #' |
|
| 35 | -! | +
- js_files <- list.files(system.file("js", package = "teal", mustWork = TRUE), pattern = pattern, full.names = TRUE)
+ #' @return |
|
| 36 | -! | +
- js_files <- js_files[!(basename(js_files) %in% except)] # no-op if except is NULL+ #' A `teal_slices` object. |
|
| 37 |
-
+ #' |
||
| 38 | -! | +
- singleton(lapply(js_files, includeScript))+ #' @seealso [`teal.slice::teal_slices`], [`teal.slice::teal_slice`], [slices_store()] |
|
| 39 |
- }+ #' |
||
| 40 |
-
+ #' @examples |
||
| 41 |
- #' Run `JS` file from `/inst/js/` package directory+ #' filter <- teal_slices( |
||
| 42 |
- #'+ #' teal_slice(dataname = "iris", varname = "Species", id = "species"), |
||
| 43 |
- #' This is triggered from the server to execute on the client+ #' teal_slice(dataname = "iris", varname = "Sepal.Length", id = "sepal_length"), |
||
| 44 |
- #' rather than triggered directly on the client.+ #' teal_slice( |
||
| 45 |
- #' Unlike `include_js_files` which includes `JavaScript` functions,+ #' dataname = "iris", id = "long_petals", title = "Long petals", expr = "Petal.Length > 5" |
||
| 46 |
- #' the `run_js` actually executes `JavaScript` functions.+ #' ), |
||
| 47 |
- #'+ #' teal_slice(dataname = "mtcars", varname = "mpg", id = "mtcars_mpg"), |
||
| 48 |
- #' `system.file` should not be used to access files in other packages, it does+ #' mapping = list( |
||
| 49 |
- #' not work with `devtools`. Therefore, we redefine this method in each package+ #' module1 = c("species", "sepal_length"),
|
||
| 50 |
- #' as needed. Thus, we do not export this method.+ #' module2 = c("mtcars_mpg"),
|
||
| 51 |
- #'+ #' global_filters = "long_petals" |
||
| 52 |
- #' @param files (`character`) vector of filenames.+ #' ) |
||
| 53 |
- #'+ #' ) |
||
| 54 |
- #' @return `NULL`, invisibly.+ #' |
||
| 55 |
- #' @keywords internal+ #' app <- init( |
||
| 56 |
- run_js_files <- function(files) {
+ #' data = teal_data(iris = iris, mtcars = mtcars), |
||
| 57 | -78x - | +
- checkmate::assert_character(files, min.len = 1, any.missing = FALSE)+ #' modules = list( |
|
| 58 | -78x - | +
- lapply(files, function(file) {
+ #' module("module1"),
|
|
| 59 | -78x - | +
- shinyjs::runjs(paste0(readLines(system.file("js", file, package = "teal", mustWork = TRUE)), collapse = "\n"))
+ #' module("module2")
|
|
| 60 |
- })+ #' ), |
||
| 61 | -78x - | +
- invisible(NULL)+ #' filter = filter |
|
| 62 |
- }+ #' ) |
||
| 63 |
-
+ #' |
||
| 64 |
- #' Code to include `teal` `CSS` and `JavaScript` files+ #' if (interactive()) {
|
||
| 65 |
- #'+ #' shinyApp(app$ui, app$server) |
||
| 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+ #' @export |
||
| 69 |
- #' styles.+ teal_slices <- function(..., |
||
| 70 |
- #' Also initializes `shinyjs` so you can use it.+ exclude_varnames = NULL, |
||
| 71 |
- #'+ include_varnames = NULL, |
||
| 72 |
- #' Simply add `include_teal_css_js()` as one of the UI elements.+ count_type = NULL, |
||
| 73 |
- #' @return A `shiny.tag.list`.+ allow_add = TRUE, |
||
| 74 |
- #' @keywords internal+ module_specific = FALSE, |
||
| 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 | -- |
- #' `teal_data` utils- |
- ||
| 2 | -- |
- #'- |
- ||
| 3 | -- |
- #' In `teal` we need to recreate the `teal_data` object due to two operations:- |
- ||
| 4 | -- |
- #' - we need to append filter-data code and objects which have been evaluated in `FilteredData` and- |
- ||
| 5 | -- |
- #' we want to avoid double-evaluation.- |
- ||
| 6 | -- |
- #' - we need to subset `teal_data` to `datanames` used by the module, to shorten obtainable R-code- |
- ||
| 7 | -- |
- #'- |
- ||
| 8 | -- |
- #' Due to above recreation of `teal_data` object can't be done simply by using public- |
- ||
| 9 | -- |
- #' `teal.code` and `teal.data` methods.- |
- ||
| 10 | -- |
- #'- |
- ||
| 11 | -- |
- #' @param data (`teal_data`)- |
- ||
| 12 | -- |
- #' @param code (`character`) code to append to `data@code`- |
- ||
| 13 | -- |
- #' @param objects (`list`) objects to append to `data@env`- |
- ||
| 14 | -- |
- #' @param datanames (`character`) names of the datasets- |
- ||
| 15 | -- |
- #' @return modified `teal_data`- |
- ||
| 16 | -- |
- #' @keywords internal- |
- ||
| 17 | -- |
- #' @name teal_data_utilities- |
- ||
| 18 | -- |
- NULL- |
- ||
| 19 | -- | - - | -||
| 20 | -- |
- #' @rdname teal_data_utilities- |
- ||
| 21 | -- |
- .append_evaluated_code <- function(data, code) {
- |
- ||
| 22 | -79x - | -
- checkmate::assert_class(data, "teal_data")- |
- ||
| 23 | -79x - | -
- data@code <- c(data@code, code)- |
- ||
| 24 | -79x - | -
- data@id <- c(data@id, max(data@id) + 1L + seq_along(code))- |
- ||
| 25 | -79x - | -
- data@messages <- c(data@messages, rep("", length(code)))
- |
- ||
| 26 | -79x - | -
- data@warnings <- c(data@warnings, rep("", length(code)))
- |
- ||
| 27 | -79x - | -
- methods::validObject(data)- |
- ||
| 28 | -79x - | -
- data- |
- ||
| 29 | -- |
- }- |
- ||
| 30 | -- | - - | -||
| 31 | -- |
- #' @rdname teal_data_utilities+ mapping, |
||
| 32 | +76 |
- .append_modified_data <- function(data, objects) {
- |
- ||
| 33 | -79x - | -
- checkmate::assert_class(data, "teal_data")+ app_id = NULL) {
|
||
| 34 | -79x - | +77 | +159x |
- checkmate::assert_class(objects, "list")+ shiny::isolate({
|
| 35 | -79x - | +78 | +159x |
- new_env <- list2env(objects, parent = .GlobalEnv)+ checkmate::assert_flag(allow_add) |
| 36 | -79x - | +79 | +159x |
- rlang::env_coalesce(new_env, teal.code::get_env(data))+ checkmate::assert_flag(module_specific) |
| 37 | -79x - | +80 | +51x |
- data@env <- new_env+ if (!missing(mapping)) checkmate::assert_list(mapping, types = c("character", "NULL"), names = "named")
|
| 38 | -79x - | +81 | +156x |
- data+ checkmate::assert_string(app_id, null.ok = TRUE) |
| 39 | +82 |
- }+ |
||
| 40 | -+ | |||
| 83 | +156x |
-
+ slices <- list(...) |
||
| 41 | -+ | |||
| 84 | +156x |
- #' @rdname teal_data_utilities+ all_slice_id <- vapply(slices, `[[`, character(1L), "id") |
||
| 42 | +85 |
- .subset_teal_data <- function(data, datanames) {
+
|
||
| 43 | -78x - | +86 | +156x |
- checkmate::assert_class(data, "teal_data")+ if (missing(mapping)) {
|
| 44 | -78x - | +87 | +108x |
- checkmate::assert_class(datanames, "character")+ mapping <- if (length(all_slice_id)) {
|
| 45 | -78x - | +88 | +26x |
- datanames_corrected <- intersect(datanames, ls(teal.code::get_env(data)))+ list(global_filters = all_slice_id) |
| 46 | -78x - | +|||
| 89 | +
- datanames_corrected_with_raw <- c(datanames_corrected, ".raw_data")+ } else {
|
|||
| 47 | -78x - | +90 | +82x |
- if (!length(datanames_corrected)) {
+ list() |
| 48 | -1x - | +|||
| 91 | +
- return(teal_data())+ } |
|||
| 49 | +92 |
- }+ } |
||
| 50 | +93 | |||
| 51 | -77x - | +94 | +156x |
- new_data <- do.call(+ if (!module_specific) {
|
| 52 | -77x - | +95 | +137x |
- teal.data::teal_data,+ mapping[setdiff(names(mapping), "global_filters")] <- NULL |
| 53 | -77x - | +|||
| 96 | +
- args = c(+ } |
|||
| 54 | -77x - | +|||
| 97 | +
- mget(x = datanames_corrected_with_raw, envir = teal.code::get_env(data)),+ |
|||
| 55 | -77x - | +98 | +156x |
- list(+ failed_slice_id <- setdiff(unlist(mapping), all_slice_id) |
| 56 | -77x - | +99 | +156x |
- code = teal.code::get_code(data, names = datanames_corrected_with_raw),+ if (length(failed_slice_id)) {
|
| 57 | -77x - | -
- join_keys = teal.data::join_keys(data)[datanames_corrected]- |
- ||
| 58 | -- |
- )- |
- ||
| 59 | -- |
- )- |
- ||
| 60 | -+ | 100 | +1x |
- )+ stop(sprintf( |
| 61 | -77x - | +101 | +1x |
- new_data@verified <- data@verified+ "Filters in mapping don't match any available filter.\n %s not in %s", |
| 62 | -77x - | +102 | +1x |
- teal.data::datanames(new_data) <- datanames_corrected+ toString(failed_slice_id), |
| 63 | -77x - | +103 | +1x |
- new_data+ toString(all_slice_id) |
| 64 | +104 |
- }+ )) |
| 1 | +105 |
- #' Store and restore `teal_slices` object+ } |
||||
| 2 | +106 |
- #'+ |
||||
| 3 | -+ | |||||
| 107 | +155x |
- #' Functions that write a `teal_slices` object to a file in the `JSON` format,+ tss <- teal.slice::teal_slices( |
||||
| 4 | +108 |
- #' and also restore the object from disk.+ ..., |
||||
| 5 | -+ | |||||
| 109 | +155x |
- #'+ exclude_varnames = exclude_varnames, |
||||
| 6 | -+ | |||||
| 110 | +155x |
- #' Date and date time objects are stored in the following formats:+ include_varnames = include_varnames, |
||||
| 7 | -+ | |||||
| 111 | +155x |
- #'+ count_type = count_type, |
||||
| 8 | -+ | |||||
| 112 | +155x |
- #' - `Date` class is converted to the `"ISO8601"` standard (`YYYY-MM-DD`).+ allow_add = allow_add |
||||
| 9 | +113 |
- #' - `POSIX*t` classes are converted to character by using+ ) |
||||
| 10 | -+ | |||||
| 114 | +155x |
- #' `format.POSIX*t(usetz = TRUE, tz = "UTC")` (`YYYY-MM-DD HH:MM:SS UTC`, where+ attr(tss, "mapping") <- mapping |
||||
| 11 | -+ | |||||
| 115 | +155x |
- #' `UTC` is the `Coordinated Universal Time` timezone short-code).+ attr(tss, "module_specific") <- module_specific |
||||
| 12 | -+ | |||||
| 116 | +155x |
- #'+ attr(tss, "app_id") <- app_id |
||||
| 13 | -+ | |||||
| 117 | +155x |
- #' This format is assumed during `slices_restore`. All `POSIX*t` objects in+ class(tss) <- c("modules_teal_slices", class(tss))
|
||||
| 14 | -+ | |||||
| 118 | +155x |
- #' `selected` or `choices` fields of `teal_slice` objects are always printed in+ tss |
||||
| 15 | +119 |
- #' `UTC` timezone as well.+ }) |
||||
| 16 | +120 |
- #'+ } |
||||
| 17 | +121 |
- #' @param tss (`teal_slices`) object to be stored.+ |
||||
| 18 | +122 |
- #' @param file (`character(1)`) file path where `teal_slices` object will be+ |
||||
| 19 | +123 |
- #' saved and restored. The file extension should be `".json"`.+ #' @rdname teal_slices |
||||
| 20 | +124 |
- #'+ #' @export |
||||
| 21 | +125 |
- #' @return `slices_store` returns `NULL`, invisibly.+ #' @keywords internal |
||||
| 22 | +126 |
#' |
||||
| 23 | +127 |
- #' @seealso [teal_slices()]+ as.teal_slices <- function(x) { # nolint: object_name.
|
||||
| 24 | -+ | |||||
| 128 | +13x |
- #'+ checkmate::assert_list(x) |
||||
| 25 | -+ | |||||
| 129 | +13x |
- #' @keywords internal+ lapply(x, checkmate::assert_list, names = "named", .var.name = "list element") |
||||
| 26 | +130 |
- #'+ |
||||
| 27 | -+ | |||||
| 131 | +13x |
- slices_store <- function(tss, file) {
+ attrs <- attributes(unclass(x)) |
||||
| 28 | -9x - | +132 | +13x |
- checkmate::assert_class(tss, "teal_slices")+ ans <- lapply(x, function(x) if (is.teal_slice(x)) x else as.teal_slice(x)) |
||
| 29 | -9x - | +133 | +13x |
- checkmate::assert_path_for_output(file, overwrite = TRUE, extension = "json")+ do.call(teal_slices, c(ans, attrs)) |
||
| 30 | +134 |
-
+ } |
||||
| 31 | -9x - | +|||||
| 135 | +
- cat(format(tss, trim_lines = FALSE), "\n", file = file)+ |
|||||
| 32 | +136 |
- }+ |
||||
| 33 | +137 |
-
+ #' @rdname teal_slices |
||||
| 34 | +138 |
- #' @rdname slices_store+ #' @export |
||||
| 35 | +139 |
- #' @return `slices_restore` returns a `teal_slices` object restored from the file.+ #' @keywords internal |
||||
| 36 | +140 |
- #' @keywords internal+ #' |
||||
| 37 | +141 |
- slices_restore <- function(file) {
+ c.teal_slices <- function(...) {
|
||||
| 38 | -9x - | +142 | +6x |
- checkmate::assert_file_exists(file, access = "r", extension = "json")+ x <- list(...)+ |
+ ||
| 143 | +6x | +
+ checkmate::assert_true(all(vapply(x, is.teal_slices, logical(1L))), .var.name = "all arguments are teal_slices") |
||||
| 39 | +144 | |||||
| 40 | -9x - | +145 | +6x |
- tss_json <- jsonlite::fromJSON(file, simplifyDataFrame = FALSE)+ all_attributes <- lapply(x, attributes) |
||
| 41 | -9x - | +146 | +6x |
- tss_json$slices <-+ all_attributes <- coalesce_r(all_attributes) |
||
| 42 | -9x - | +147 | +6x |
- lapply(tss_json$slices, function(slice) {
+ all_attributes <- all_attributes[names(all_attributes) != "class"]+ |
+ ||
| 148 | ++ | + | ||||
| 43 | -9x - | +149 | +6x |
- for (field in c("selected", "choices")) {
+ do.call( |
||
| 44 | -18x - | +150 | +6x |
- if (!is.null(slice[[field]])) {
+ teal_slices, |
||
| 45 | -12x - | +151 | +6x |
- if (length(slice[[field]]) > 0) {
+ c( |
||
| 46 | -9x - | +152 | +6x |
- date_partial_regex <- "^[0-9]{4}-[0-9]{2}-[0-9]{2}"
+ unique(unlist(x, recursive = FALSE)), |
||
| 47 | -9x - | +153 | +6x |
- time_stamp_regex <- paste0(date_partial_regex, "\\s[0-9]{2}:[0-9]{2}:[0-9]{2}\\sUTC$")
+ all_attributes |
||
| 48 | +154 |
-
+ ) |
||||
| 49 | -9x - | +|||||
| 155 | +
- slice[[field]] <-+ ) |
|||||
| 50 | -9x - | +|||||
| 156 | +
- if (all(grepl(paste0(date_partial_regex, "$"), slice[[field]]))) {
+ } |
|||||
| 51 | -3x - | +|||||
| 157 | +
- as.Date(slice[[field]])+ |
|||||
| 52 | -9x - | +|||||
| 158 | +
- } else if (all(grepl(time_stamp_regex, slice[[field]]))) {
+
|
|||||
| 53 | -3x - | +|||||
| 159 | +
- as.POSIXct(slice[[field]], tz = "UTC")+ #' Deep copy `teal_slices` |
|||||
| 54 | +160 |
- } else {
+ #' |
||||
| 55 | -3x - | +|||||
| 161 | +
- slice[[field]]+ #' it's important to create a new copy of `teal_slices` when |
|||||
| 56 | +162 |
- }+ #' starting a new `shiny` session. Otherwise, object will be shared |
||||
| 57 | +163 |
- } else {
+ #' by multiple users as it is created in global environment before |
||||
| 58 | -3x - | +|||||
| 164 | +
- slice[[field]] <- character(0)+ #' `shiny` session starts. |
|||||
| 59 | +165 |
- }+ #' @param filter (`teal_slices`) |
||||
| 60 | +166 |
- }+ #' @return `teal_slices` |
||||
| 61 | +167 |
- }+ #' @keywords internal+ |
+ ||||
| 168 | ++ |
+ deep_copy_filter <- function(filter) {
|
||||
| 62 | -9x - | +169 | +1x |
- slice+ checkmate::assert_class(filter, "teal_slices") |
||
| 63 | -+ | |||||
| 170 | +1x |
- })+ shiny::isolate({
|
||||
| 64 | -+ | |||||
| 171 | +1x |
-
+ filter_copy <- lapply(filter, function(slice) {
|
||||
| 65 | -9x - | +172 | +2x |
- tss_elements <- lapply(tss_json$slices, as.teal_slice)+ teal.slice::as.teal_slice(as.list(slice)) |
||
| 66 | +173 |
-
+ }) |
||||
| 67 | -9x - | +174 | +1x |
- do.call(teal_slices, c(tss_elements, tss_json$attributes))+ attributes(filter_copy) <- attributes(filter)+ |
+ ||
| 175 | +1x | +
+ filter_copy |
||||
| 68 | +176 | ++ |
+ })+ |
+ |||
| 177 |
}@@ -43502,40 +41505,35 @@ teal coverage - 59.73% | |||||
| 57 | -76x - | +79x |
assert_reactive(teal_data) |
|||
| 58 | -76x - | +79x |
moduleServer( |
|||
| 59 | -76x - | +79x |
id = id, |
|||
| 60 | -76x - | +79x |
function(input, output, session) {
|
|||
| 61 | -76x - | +79x |
logger::log_debug("srv_data_summary initializing")
|
@@ -43549,32 +41547,28 @@ |||
| 63 | -76x - | +79x |
summary_table <- reactive({
|
|||
| 64 | -84x - | +87x |
req(inherits(teal_data(), "teal_data")) |
|||
| 65 | -78x - | +81x |
if (!length(ls(teal.code::get_env(teal_data())))) {
|
|||
| 66 | -1x - | +2x |
return(NULL) |
@@ -43595,16 +41589,14 @@ |||
| 69 | -77x - | +79x |
filter_overview <- get_filter_overview(teal_data) |
|||
| 70 | -77x - | +79x |
names(filter_overview)[[1]] <- "Data Name" |
@@ -43618,32 +41610,28 @@ |||
| 72 | -77x - | +79x |
filter_overview$Obs <- ifelse( |
|||
| 73 | -77x - | +79x |
!is.na(filter_overview$obs), |
|||
| 74 | -77x - | +79x |
sprintf("%s/%s", filter_overview$obs_filtered, filter_overview$obs),
|
|||
| 75 | -77x - | +79x |
ifelse(!is.na(filter_overview$obs_filtered), sprintf("%s", filter_overview$obs_filtered), "")
|
@@ -43664,24 +41652,21 @@ |||
| 78 | -77x - | +79x |
filter_overview$Subjects <- ifelse( |
|||
| 79 | -77x - | +79x |
!is.na(filter_overview$subjects), |
|||
| 80 | -77x - | +79x |
sprintf("%s/%s", filter_overview$subjects_filtered, filter_overview$subjects),
|
@@ -43709,16 +41694,14 @@ |||
| 84 | -77x - | +79x |
filter_overview <- filter_overview[, colnames(filter_overview) %in% c("Data Name", "Obs", "Subjects")]
|
|||
| 85 | -77x - | +79x |
Filter(function(col) !all(col == ""), filter_overview) |
@@ -43739,24 +41722,21 @@ |||
| 88 | -76x - | +79x |
output$table <- renderUI({
|
|||
| 89 | -84x - | +87x |
summary_table_out <- try(summary_table(), silent = TRUE) |
|||
| 90 | -84x - | +87x |
if (inherits(summary_table_out, "try-error")) {
|
@@ -43770,8 +41750,7 @@ |||
| 92 | -6x - | +6x |
if (!inherits(attr(summary_table_out, "condition"), "shiny.silent.error")) {
|
@@ -43792,16 +41771,14 @@ |||
| 95 | -78x - | +81x |
} else if (is.null(summary_table_out)) {
|
|||
| 96 | -1x - | +2x |
"no datasets to show" |
@@ -43815,112 +41792,98 @@ |||
| 98 | -77x - | +79x |
body_html <- apply( |
|||
| 99 | -77x - | +79x |
summary_table_out, |
|||
| 100 | -77x - | +79x |
1, |
|||
| 101 | -77x - | +79x |
function(x) {
|
|||
| 102 | -139x - | +142x |
tags$tr( |
|||
| 103 | -139x - | +142x |
tagList( |
|||
| 104 | -139x - | +142x |
tags$td( |
|||
| 105 | -139x - | +142x |
if (all(x[-1] == "")) {
|
|||
| 106 | -5x - | +5x |
icon( |
|||
| 107 | -5x - | +5x |
name = "fas fa-exclamation-triangle", |
|||
| 108 | -5x - | +5x |
title = "Unsupported dataset", |
|||
| 109 | -5x - | +5x |
`data-container` = "body", |
|||
| 110 | -5x - | +5x |
`data-toggle` = "popover", |
|||
| 111 | -5x - | +5x |
`data-content` = "object not supported by the data_summary module" |
@@ -43941,8 +41904,7 @@ |||
| 114 | -139x - | +142x |
x[1] |
@@ -43956,8 +41918,7 @@ |||
| 116 | -139x - | +142x |
lapply(x[-1], tags$td) |
@@ -43999,16 +41960,14 @@ |||
| 122 | -77x - | +79x |
header_labels <- names(summary_table()) |
|||
| 123 | -77x - | +79x |
header_html <- tags$tr(tagList(lapply(header_labels, tags$td))) |
@@ -44022,32 +41981,28 @@ |||
| 125 | -77x - | +79x |
table_html <- tags$table( |
|||
| 126 | -77x - | +79x |
class = "table custom-table", |
|||
| 127 | -77x - | +79x |
tags$thead(header_html), |
|||
| 128 | -77x - | +79x |
tags$tbody(body_html) |
@@ -44061,8 +42016,7 @@ |||
| 130 | -77x - | +79x |
table_html |
@@ -44090,8 +42044,7 @@ |||
| 134 | -76x - | +79x |
summary_table # testing purpose |
@@ -44140,16 +42093,14 @@ |||
| 141 | -77x - | +79x |
datanames <- teal.data::datanames(teal_data()) |
|||
| 142 | -77x - | +79x |
joinkeys <- teal.data::join_keys(teal_data()) |
@@ -44163,32 +42114,28 @@ |||
| 144 | -77x - | +79x |
filtered_data_objs <- sapply( |
|||
| 145 | -77x - | +79x |
datanames, |
|||
| 146 | -77x - | +79x |
function(name) teal.code::get_var(teal_data(), name), |
|||
| 147 | -77x - | +79x |
simplify = FALSE |
@@ -44202,8 +42149,7 @@ |||
| 149 | -77x - | +79x |
unfiltered_data_objs <- teal.code::get_var(teal_data(), ".raw_data") |
@@ -44217,32 +42163,28 @@ |||
| 151 | -77x - | +79x |
rows <- lapply( |
|||
| 152 | -77x - | +79x |
datanames, |
|||
| 153 | -77x - | +79x |
function(dataname) {
|
|||
| 154 | -139x - | +142x |
parent <- teal.data::parent(joinkeys, dataname) |
@@ -44291,16 +42233,14 @@ |||
| 161 | -139x - | +142x |
subject_keys <- if (length(parent) > 0) {
|
|||
| 162 | -7x - | +7x |
names(joinkeys[dataname, parent]) |
@@ -44314,8 +42254,7 @@ |||
| 164 | -132x - | +135x |
joinkeys[dataname, dataname] |
@@ -44329,40 +42268,35 @@ |||
| 166 | -139x - | +142x |
get_object_filter_overview( |
|||
| 167 | -139x - | +142x |
filtered_data = filtered_data_objs[[dataname]], |
|||
| 168 | -139x - | +142x |
unfiltered_data = unfiltered_data_objs[[dataname]], |
|||
| 169 | -139x - | +142x |
dataname = dataname, |
|||
| 170 | -139x - | +142x |
subject_keys = subject_keys |
@@ -44397,16 +42331,14 @@ |||
| 175 | -77x - | +79x |
unssuported_idx <- vapply(rows, function(x) all(is.na(x[-1])), logical(1)) # this is mainly for vectors |
|||
| 176 | -77x - | +79x |
do.call(rbind, c(rows[!unssuported_idx], rows[unssuported_idx])) |
@@ -44462,24 +42394,21 @@ |||
| 184 | -139x - | +142x |
if (inherits(filtered_data, c("data.frame", "DataFrame", "array", "Matrix", "SummarizedExperiment"))) {
|
|||
| 185 | -134x - | +137x |
get_object_filter_overview_array(filtered_data, unfiltered_data, dataname, subject_keys) |
|||
| 186 | -5x - | +5x |
} else if (inherits(filtered_data, "MultiAssayExperiment")) {
|
@@ -44500,48 +42429,42 @@ |||
| 189 | -5x - | +5x |
data.frame( |
|||
| 190 | -5x - | +5x |
dataname = dataname, |
|||
| 191 | -5x - | +5x |
obs = NA, |
|||
| 192 | -5x - | +5x |
obs_filtered = NA, |
|||
| 193 | -5x - | +5x |
subjects = NA, |
|||
| 194 | -5x - | +5x |
subjects_filtered = NA |
@@ -44611,56 +42534,49 @@ |||
| 204 | -134x - | +137x |
if (length(subject_keys) == 0) {
|
|||
| 205 | -121x - | +124x |
data.frame( |
|||
| 206 | -121x - | +124x |
dataname = dataname, |
|||
| 207 | -121x - | +124x |
obs = ifelse(!is.null(nrow(unfiltered_data)), nrow(unfiltered_data), NA), |
|||
| 208 | -121x - | +124x |
obs_filtered = nrow(filtered_data), |
|||
| 209 | -121x - | +124x |
subjects = NA, |
|||
| 210 | -121x - | +124x |
subjects_filtered = NA |
@@ -44681,48 +42597,42 @@ |||
| 213 | -13x - | +13x |
data.frame( |
|||
| 214 | -13x - | +13x |
dataname = dataname, |
|||
| 215 | -13x - | +13x |
obs = ifelse(!is.null(nrow(unfiltered_data)), nrow(unfiltered_data), NA), |
|||
| 216 | -13x - | +13x |
obs_filtered = nrow(filtered_data), |
|||
| 217 | -13x - | +13x |
subjects = nrow(unique(unfiltered_data[subject_keys])), |
|||
| 218 | -13x - | +13x |
subjects_filtered = nrow(unique(filtered_data[subject_keys])) |
@@ -45004,74 +42914,353 @@ 258 | ! |
- function(experiment_name) {
+ function(experiment_name) {
+ |
+
| 259 | +! | +
+ data.frame(+ |
+ ||||
| 260 | +! | +
+ subjects = get_experiment_keys(filtered_data, unfiltered_data[[experiment_name]]),+ |
+ ||||
| 261 | +! | +
+ subjects_filtered = get_experiment_keys(filtered_data, filtered_data[[experiment_name]])+ |
+ ||||
| 262 | ++ |
+ )+ |
+ ||||
| 263 | ++ |
+ }+ |
+ ||||
| 264 | ++ |
+ ))+ |
+ ||||
| 265 | ++ | + + | +||||
| 266 | +! | +
+ experiment_info <- cbind(experiment_obs_info[, c("dataname", "obs", "obs_filtered")], experiment_subjects_info)
+ |
+ ||||
| 267 | +! | +
+ rbind(mae_info, experiment_info)+ |
+ ||||
| 268 | ++ |
+ }+ |
+
| 1 | ++ |
+ #' UI and server modules of `teal`+ |
+ ||||
| 2 | ++ |
+ #'+ |
+ ||||
| 3 | ++ |
+ #' @description `r lifecycle::badge("deprecated")`
+ |
+ ||||
| 4 | ++ |
+ #' Please use [`module_teal`] instead.+ |
+ ||||
| 5 | ++ |
+ #'+ |
+ ||||
| 6 | ++ |
+ #' @inheritParams ui_teal+ |
+ ||||
| 7 | ++ |
+ #' @inheritParams srv_teal+ |
+ ||||
| 8 | ++ |
+ #'+ |
+ ||||
| 9 | ++ |
+ #' @return+ |
+ ||||
| 10 | ++ |
+ #' Returns a `reactive` expression containing a `teal_data` object when data is loaded or `NULL` when it is not.+ |
+ ||||
| 11 | ++ |
+ #' @name module_teal_with_splash+ |
+ ||||
| 12 | ++ |
+ #'+ |
+ ||||
| 13 | ++ |
+ NULL+ |
+ ||||
| 14 | ++ | + + | +||||
| 15 | ++ |
+ #' @export+ |
+ ||||
| 16 | ++ |
+ #' @rdname module_teal_with_splash+ |
+ ||||
| 17 | ++ |
+ ui_teal_with_splash <- function(id,+ |
+ ||||
| 18 | ++ |
+ data,+ |
+ ||||
| 19 | ++ |
+ title = build_app_title(),+ |
+ ||||
| 20 | ++ |
+ header = tags$p(),+ |
+ ||||
| 21 | ++ |
+ footer = tags$p()) {
+ |
+ ||||
| 22 | +! | +
+ lifecycle::deprecate_soft(+ |
+ ||||
| 23 | +! | +
+ when = "0.16",+ |
+ ||||
| 24 | +! | +
+ what = "ui_teal_with_splash()",+ |
+ ||||
| 25 | +! | +
+ details = "Deprecated, please use `ui_teal` instead"+ |
+ ||||
| 26 | ++ |
+ ) |
||||
| 259 | +27 | ! |
- data.frame(+ ui_teal(id = id, title = title, header = header, footer = footer) |
|||
| 260 | -! | +|||||
| 28 | +
- subjects = get_experiment_keys(filtered_data, unfiltered_data[[experiment_name]]),+ } |
|||||
| 261 | -! | +|||||
| 29 | +
- subjects_filtered = get_experiment_keys(filtered_data, filtered_data[[experiment_name]])+ |
|||||
| 262 | +30 |
- )+ #' @export |
||||
| 263 | +31 |
- }+ #' @rdname module_teal_with_splash |
||||
| 264 | +32 |
- ))+ srv_teal_with_splash <- function(id, data, modules, filter = teal_slices()) {
|
||||
| 265 | -+ | |||||
| 33 | +! |
-
+ lifecycle::deprecate_soft( |
||||
| 266 | +34 | ! |
- experiment_info <- cbind(experiment_obs_info[, c("dataname", "obs", "obs_filtered")], experiment_subjects_info)
+ when = "0.16", |
|||
| 267 | +35 | ! |
- rbind(mae_info, experiment_info)+ what = "srv_teal_with_splash()",+ |
+ |||
| 36 | +! | +
+ details = "Deprecated, please use `srv_teal` instead" |
||||
| 268 | +37 | ++ |
+ )+ |
+ |||
| 38 | +! | +
+ srv_teal(id = id, data = data, modules = modules, filter = filter)+ |
+ ||||
| 39 |
}@@ -45365,40 +43554,35 @@ teal coverage - 59.73% | |||||
| 41 | -9x - | +9x |
ns <- shiny::NS(id) |
|||
| 42 | -9x - | +9x |
shiny::div( |
|||
| 43 | -9x - | +9x |
id = ns("content"),
|
|||
| 44 | -9x - | +9x |
style = "display: inline-block; width: 100%;", |
|||
| 45 | -9x - | +9x |
uiOutput(ns("data"))
|
@@ -45440,16 +43624,14 @@ |||
| 51 | -78x - | +81x |
checkmate::assert_character(id, max.len = 1, any.missing = FALSE) |
|||
| 52 | -78x - | +81x |
checkmate::assert_multi_class(data, c("teal_data", "teal_data_module", "reactive"))
|
@@ -45463,16 +43645,14 @@ |||
| 54 | -78x - | +81x |
moduleServer(id, function(input, output, session) {
|
|||
| 55 | -78x - | +81x |
logger::log_debug("srv_data initializing.")
|
@@ -45493,56 +43673,49 @@ |||
| 58 | -78x - | +81x |
data_out <- if (inherits(data, "teal_data_module")) {
|
|||
| 59 | -10x - | +10x |
output$data <- renderUI(data$ui(id = session$ns("teal_data_module")))
|
|||
| 60 | -10x - | +10x |
data$server("teal_data_module")
|
|||
| 61 | -78x - | +81x |
} else if (inherits(data, "teal_data")) {
|
|||
| 62 | -39x - | +41x |
reactiveVal(data) |
|||
| 63 | -78x - | +81x |
} else if (test_reactive(data)) {
|
|||
| 64 | -29x - | +30x |
data |
@@ -45563,16 +43736,14 @@ |||
| 67 | -77x - | +80x |
data_handled <- reactive({
|
|||
| 68 | -70x - | +73x |
tryCatch(data_out(), error = function(e) e) |
@@ -45600,72 +43771,63 @@ |||
| 72 | -77x - | +80x |
observeEvent(data_handled(), {
|
|||
| 73 | -70x - | +73x |
if (inherits(data_handled(), "teal_data")) {
|
|||
| 74 | -65x - | +68x |
app_session <- .subset2(shiny::getDefaultReactiveDomain(), "parent") |
|||
| 75 | -65x - | +68x |
setBookmarkExclude( |
|||
| 76 | -65x - | +68x |
session$ns( |
|||
| 77 | -65x - | +68x |
grep( |
|||
| 78 | -65x - | +68x |
pattern = "teal_data_module-", |
|||
| 79 | -65x - | +68x |
x = names(reactiveValuesToList(input)), |
|||
| 80 | -65x - | +68x |
value = TRUE |
@@ -45686,8 +43848,7 @@ |||
| 83 | -65x - | +68x |
session = app_session |
@@ -45722,8 +43883,7 @@ |||
| 88 | -77x - | +80x |
data_handled |
@@ -45786,8 +43946,7 @@ |||
| 97 | -65x - | +68x |
hashes <- .get_hashes_code(data) |
@@ -45801,80 +43960,70 @@ |||
| 99 | -65x - | +68x |
tdata <- do.call( |
|||
| 100 | -65x - | +68x |
teal.data::teal_data, |
|||
| 101 | -65x - | +68x |
c( |
|||
| 102 | -65x - | +68x |
list(code = trimws(c(teal.code::get_code(data), hashes), which = "right")), |
|||
| 103 | -65x - | +68x |
list(join_keys = teal.data::join_keys(data)), |
|||
| 104 | -65x - | +68x |
sapply( |
|||
| 105 | -65x - | +68x |
ls(teal.code::get_env(data)), |
|||
| 106 | -65x - | +68x |
teal.code::get_var, |
|||
| 107 | -65x - | +68x |
object = data, |
|||
| 108 | -65x - | +68x |
simplify = FALSE |
@@ -45909,16 +44058,14 @@ |||
| 113 | -65x - | +68x |
tdata@verified <- data@verified |
|||
| 114 | -65x - | +68x |
tdata |
@@ -45976,194 +44123,661 @@ 122 |
- #' @return A character vector with the code lines.+ #' @return A character vector with the code lines.+ |
+ |
| 123 | ++ |
+ #' @keywords internal+ |
+ ||||
| 124 | ++ |
+ #'+ |
+ ||||
| 125 | ++ |
+ .get_hashes_code <- function(data, datanames = ls(teal.code::get_env(data))) {
+ |
+ ||||
| 126 | +68x | +
+ vapply(+ |
+ ||||
| 127 | +68x | +
+ datanames,+ |
+ ||||
| 128 | +68x | +
+ function(dataname, datasets) {
+ |
+ ||||
| 129 | +119x | +
+ x <- data[[dataname]]+ |
+ ||||
| 130 | ++ | + + | +||||
| 131 | +119x | +
+ code <- if (is.function(x) && !is.primitive(x)) {
+ |
+ ||||
| 132 | +4x | +
+ x <- deparse1(x)+ |
+ ||||
| 133 | +4x | +
+ bquote(rlang::hash(deparse1(.(as.name(dataname)))))+ |
+ ||||
| 134 | ++ |
+ } else {
+ |
+ ||||
| 135 | +115x | +
+ bquote(rlang::hash(.(as.name(dataname))))+ |
+ ||||
| 136 | ++ |
+ }+ |
+ ||||
| 137 | +119x | +
+ sprintf(+ |
+ ||||
| 138 | +119x | +
+ "stopifnot(%s == %s) # @linksto %s",+ |
+ ||||
| 139 | +119x | +
+ deparse1(code),+ |
+ ||||
| 140 | +119x | +
+ deparse1(rlang::hash(x)),+ |
+ ||||
| 141 | +119x | +
+ dataname+ |
+ ||||
| 142 | ++ |
+ )+ |
+ ||||
| 143 | ++ |
+ },+ |
+ ||||
| 144 | +68x | +
+ character(1L),+ |
+ ||||
| 145 | +68x | +
+ USE.NAMES = TRUE+ |
+ ||||
| 146 | ++ |
+ )+ |
+ ||||
| 147 | ++ |
+ }+ |
+
| 1 | ++ |
+ #' Store and restore `teal_slices` object+ |
+ ||
| 2 | ++ |
+ #'+ |
+ ||
| 3 | ++ |
+ #' Functions that write a `teal_slices` object to a file in the `JSON` format,+ |
+ ||
| 4 | ++ |
+ #' and also restore the object from disk.+ |
+ ||
| 5 | ++ |
+ #'+ |
+ ||
| 6 | ++ |
+ #' Date and date time objects are stored in the following formats:+ |
+ ||
| 7 | ++ |
+ #'+ |
+ ||
| 8 | ++ |
+ #' - `Date` class is converted to the `"ISO8601"` standard (`YYYY-MM-DD`).+ |
+ ||
| 9 | ++ |
+ #' - `POSIX*t` classes are converted to character by using+ |
+ ||
| 10 | ++ |
+ #' `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 | ++ |
+ #'+ |
+ ||
| 13 | ++ |
+ #' 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 | ++ |
+ #' `UTC` timezone as well.+ |
+ ||
| 16 | ++ |
+ #'+ |
+ ||
| 17 | ++ |
+ #' @param tss (`teal_slices`) object to be stored.+ |
+ ||
| 18 | ++ |
+ #' @param file (`character(1)`) file path where `teal_slices` object will be+ |
+ ||
| 19 | ++ |
+ #' saved and restored. The file extension should be `".json"`.+ |
+ ||
| 20 | ++ |
+ #'+ |
+ ||
| 21 | ++ |
+ #' @return `slices_store` returns `NULL`, invisibly.+ |
+ ||
| 22 | ++ |
+ #'+ |
+ ||
| 23 | ++ |
+ #' @seealso [teal_slices()]+ |
+ ||
| 24 | ++ |
+ #'+ |
+ ||
| 25 | ++ |
+ #' @keywords internal+ |
+ ||
| 26 | ++ |
+ #'+ |
+ ||
| 27 | ++ |
+ slices_store <- function(tss, file) {
+ |
+ ||
| 28 | +9x | +
+ checkmate::assert_class(tss, "teal_slices")+ |
+ ||
| 29 | +9x | +
+ checkmate::assert_path_for_output(file, overwrite = TRUE, extension = "json")+ |
+ ||
| 30 | ++ | + + | +||
| 31 | +9x | +
+ cat(format(tss, trim_lines = FALSE), "\n", file = file)+ |
+ ||
| 32 | ++ |
+ }+ |
+ ||
| 33 | ++ | + + | +||
| 34 | ++ |
+ #' @rdname slices_store+ |
+ ||
| 35 | ++ |
+ #' @return `slices_restore` returns a `teal_slices` object restored from the file.+ |
+ ||
| 36 | ++ |
+ #' @keywords internal+ |
+ ||
| 37 | ++ |
+ slices_restore <- function(file) {
+ |
+ ||
| 38 | +9x | +
+ checkmate::assert_file_exists(file, access = "r", extension = "json")+ |
+ ||
| 39 | ++ | + + | +||
| 40 | +9x | +
+ tss_json <- jsonlite::fromJSON(file, simplifyDataFrame = FALSE) |
||
| 123 | -+ | |||
| 41 | +9x |
- #' @keywords internal+ tss_json$slices <- |
||
| 124 | -+ | |||
| 42 | +9x |
- #'+ lapply(tss_json$slices, function(slice) {
|
||
| 125 | -+ | |||
| 43 | +9x |
- .get_hashes_code <- function(data, datanames = ls(teal.code::get_env(data))) {
+ for (field in c("selected", "choices")) {
|
||
| 126 | -65x - | +44 | +18x |
- vapply(+ if (!is.null(slice[[field]])) {
|
| 127 | -65x - | +45 | +12x |
- datanames,+ if (length(slice[[field]]) > 0) {
|
| 128 | -65x - | +46 | +9x |
- function(dataname, datasets) {
+ date_partial_regex <- "^[0-9]{4}-[0-9]{2}-[0-9]{2}"
|
| 129 | -115x - | +47 | +9x |
- x <- data[[dataname]]+ time_stamp_regex <- paste0(date_partial_regex, "\\s[0-9]{2}:[0-9]{2}:[0-9]{2}\\sUTC$")
|
| 130 | +48 | |||
| 131 | -115x - | +49 | +9x |
- code <- if (is.function(x) && !is.primitive(x)) {
+ slice[[field]] <- |
| 132 | -4x - | +50 | +9x |
- x <- deparse1(x)+ if (all(grepl(paste0(date_partial_regex, "$"), slice[[field]]))) {
|
| 133 | -4x - | +51 | +3x |
- bquote(rlang::hash(deparse1(.(as.name(dataname)))))+ as.Date(slice[[field]]) |
| 134 | -+ | |||
| 52 | +9x |
- } else {
+ } else if (all(grepl(time_stamp_regex, slice[[field]]))) {
|
||
| 135 | -111x - | +53 | +3x |
- bquote(rlang::hash(.(as.name(dataname))))+ as.POSIXct(slice[[field]], tz = "UTC") |
| 136 | +54 |
- }+ } else {
|
||
| 137 | -115x - | +55 | +3x |
- sprintf(+ slice[[field]] |
| 138 | -115x - | +|||
| 56 | +
- "stopifnot(%s == %s) # @linksto %s",+ } |
|||
| 139 | -115x - | +|||
| 57 | +
- deparse1(code),+ } else {
|
|||
| 140 | -115x - | +58 | +3x |
- deparse1(rlang::hash(x)),+ slice[[field]] <- character(0) |
| 141 | -115x - | +|||
| 59 | +
- dataname+ } |
|||
| 142 | +60 |
- )+ } |
||
| 143 | +61 |
- },+ } |
||
| 144 | -65x - | +62 | +9x |
- character(1L),+ slice+ |
+
| 63 | ++ |
+ })+ |
+ ||
| 64 | ++ | + | ||
| 145 | -65x - | +65 | +9x |
- USE.NAMES = TRUE+ tss_elements <- lapply(tss_json$slices, as.teal_slice) |
| 146 | +66 |
- )+ + |
+ ||
| 67 | +9x | +
+ do.call(teal_slices, c(tss_elements, tss_json$attributes)) |
||
| 147 | +68 |
}@@ -46226,32 +44840,28 @@ teal coverage - 59.73% | ||
| 8 | -1x - | +1x |
libraries <- vapply( |
|
| 9 | -1x - | +1x |
utils::sessionInfo()$otherPkgs, |
|
| 10 | -1x - | +1x |
function(x) {
|
|
| 11 | -6x - | +6x |
paste0("library(", x$Package, ")")
|
@@ -46265,8 +44875,7 @@ |
| 13 | -1x - | +1x |
character(1) |
@@ -46280,8 +44889,7 @@ |
| 15 | -1x - | +1x |
paste0(paste0(rev(libraries), sep = "\n"), collapse = "") |
@@ -46330,24 +44938,21 @@ |
| 22 | -5x - | +5x |
code_string <- getOption("teal.load_nest_code")
|
|
| 23 | -5x - | +5x |
if (is.character(code_string)) {
|
|
| 24 | -2x - | +2x |
code_string |
@@ -46361,8 +44966,7 @@ |
| 26 | -3x - | +3x |
"# Add any code to install/load your NEST environment here\n" |
@@ -46384,14 +44988,14 @@
| 1 |
- #' Evaluate expression on `teal_data_module`+ #' Create a `tdata` object |
||
| 3 |
- #' @details+ #' @description `r lifecycle::badge("superseded")`
|
||
| 4 |
- #' `within` is a convenience function for evaluating inline code inside the environment of a `teal_data_module`.+ #' |
||
| 5 |
- #' It accepts only inline expressions (both simple and compound) and allows for injecting values into `expr` through+ #' Recent changes in `teal` cause modules to fail because modules expect a `tdata` object |
||
| 6 |
- #' the `...` argument: as `name:value` pairs are passed to `...`, `name` in `expr` will be replaced with `value.`+ #' 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. |
||
| 8 |
- #' @param data (`teal_data_module`) object+ #' In order to easily adapt such modules without a proper refactor, |
||
| 9 |
- #' @param expr (`expression`) to evaluate. Must be inline code. See+ #' use this function to downgrade the `data` argument. |
||
| 10 |
- #' @param ... See `Details`.+ #' |
||
| 11 |
- #'+ #' @name tdata |
||
| 12 |
- #' @return+ #' @param ... ignored |
||
| 13 |
- #' `within` returns a `teal_data_module` object with a delayed evaluation of `expr` when the module is run.+ #' @return nothing |
||
| 14 |
- #'+ NULL |
||
| 15 |
- #' @examples+ |
||
| 16 |
- #' within(tdm, dataset1 <- subset(dataset1, Species == "virginica"))+ #' @rdname tdata |
||
| 17 |
- #'+ #' @export |
||
| 18 |
- #' # use additional parameter for expression value substitution.+ new_tdata <- function(...) {
|
||
| 19 | -+ | ! |
- #' valid_species <- "versicolor"+ .deprecate_tdata_msg() |
| 20 |
- #' within(tdm, dataset1 <- subset(dataset1, Species %in% species), species = valid_species)+ } |
||
| 21 |
- #' @include teal_data_module.R+ |
||
| 22 |
- #' @name within+ #' @rdname tdata |
||
| 23 |
- #' @rdname teal_data_module+ #' @export |
||
| 24 |
- #'+ tdata2env <- function(...) {
|
||
| 25 | -+ | ! |
- #' @export+ .deprecate_tdata_msg() |
| 26 |
- #'+ } |
||
| 27 |
- within.teal_data_module <- function(data, expr, ...) {
+
|
||
| 28 | -2x - | +
- expr <- substitute(expr)+ #' @rdname tdata |
|
| 29 | -2x - | +
- extras <- list(...)+ #' @export |
|
| 30 |
-
+ get_code_tdata <- function(...) {
|
||
| 31 | -+ | ! |
- # Add braces for consistency.+ .deprecate_tdata_msg() |
| 32 | -2x - | +
- if (!identical(as.list(expr)[[1L]], as.symbol("{"))) {
+ } |
|
| 33 | -2x - | +
- expr <- call("{", expr)
+
|
|
| 34 |
- }+ #' @rdname tdata |
||
| 35 |
-
+ #' @export |
||
| 36 | -2x - | +
- calls <- as.list(expr)[-1]+ join_keys.tdata <- function(...) {
|
|
| 37 | -+ | ! |
-
+ .deprecate_tdata_msg() |
| 38 |
- # Inject extra values into expressions.+ } |
||
| 39 | -2x - | +
- calls <- lapply(calls, function(x) do.call(substitute, list(x, env = extras)))+ |
|
| 40 |
-
+ #' @rdname tdata |
||
| 41 | -2x - | +
- eval_code(object = data, code = as.expression(calls))+ #' @export |
|
| 42 | + |
+ get_metadata <- function(...) {
+ |
+ |
| 43 | +! | +
+ .deprecate_tdata_msg()+ |
+ |
| 44 | ++ |
+ }+ |
+ |
| 45 | ++ | + + | +|
| 46 | ++ |
+ #' @rdname tdata+ |
+ |
| 47 | ++ |
+ #' @export+ |
+ |
| 48 | ++ |
+ as_tdata <- function(...) {
+ |
+ |
| 49 | +! | +
+ .deprecate_tdata_msg()+ |
+ |
| 50 | ++ |
+ }+ |
+ |
| 51 | ++ | + + | +|
| 52 | ++ | + + | +|
| 53 | ++ |
+ .deprecate_tdata_msg <- function() {
+ |
+ |
| 54 | +! | +
+ lifecycle::deprecate_stop(+ |
+ |
| 55 | +! | +
+ when = "0.16",+ |
+ |
| 56 | +! | +
+ what = "tdata()",+ |
+ |
| 57 | +! | +
+ details = paste(+ |
+ |
| 58 | +! | +
+ "tdata has been removed in favour of `teal_data`.\n",+ |
+ |
| 59 | +! | +
+ "Please follow migration instructions https://github.com/insightsengineering/teal/discussions/987."+ |
+ |
| 60 | ++ |
+ )+ |
+ |
| 61 | ++ |
+ )+ |
+ |
| 62 | +
} |
@@ -46691,14 +45428,14 @@
| 1 |
- #' UI and server modules of `teal`+ #' Show `R` code modal |
||
| 4 |
- #' Please use [`module_teal`] instead.+ #' |
||
| 5 |
- #'+ #' Use the [shiny::showModal()] function to show the `R` code inside. |
||
| 6 |
- #' @inheritParams ui_teal+ #' |
||
| 7 |
- #' @inheritParams srv_teal+ #' @param title (`character(1)`) |
||
| 8 |
- #'+ #' Title of the modal, displayed in the first comment of the `R` code. |
||
| 9 |
- #' @return+ #' @param rcode (`character`) |
||
| 10 |
- #' Returns a `reactive` expression containing a `teal_data` object when data is loaded or `NULL` when it is not.+ #' vector with `R` code to show inside the modal. |
||
| 11 |
- #' @name module_teal_with_splash+ #' @param session (`ShinySession`) optional |
||
| 12 |
- #'+ #' `shiny` session object, defaults to [shiny::getDefaultReactiveDomain()]. |
||
| 13 |
- NULL+ #' |
||
| 14 |
-
+ #' @references [shiny::showModal()] |
||
| 16 |
- #' @rdname module_teal_with_splash+ show_rcode_modal <- function(title = NULL, rcode, session = getDefaultReactiveDomain()) {
|
||
| 17 | -+ | ! |
- ui_teal_with_splash <- function(id,+ lifecycle::deprecate_soft( |
| 18 | -+ | ! |
- data,+ when = "0.16", |
| 19 | -+ | ! |
- title = build_app_title(),+ what = "show_rcode_modal()", |
| 20 | -+ | ! |
- header = tags$p(),+ details = "This function will be removed in the next release." |
| 21 |
- footer = tags$p()) {
+ ) |
||
| 22 | -! | +
- lifecycle::deprecate_soft(+ |
|
| 23 | ! |
- when = "0.16",+ rcode <- paste(rcode, collapse = "\n") |
|
| 24 | -! | +
- what = "ui_teal_with_splash()",+ |
|
| 25 | ! |
- details = "Deprecated, please use `ui_teal` instead"+ ns <- session$ns |
|
| 26 | -+ | ! |
- )+ showModal(modalDialog( |
| 27 | ! |
- ui_teal(id = id, title = title, header = header, footer = footer)+ tagList( |
|
| 28 | -+ | ! |
- }+ tags$div( |
| 29 | -+ | ! |
-
+ actionButton(ns("copyRCode"), "Copy to Clipboard", `data-clipboard-target` = paste0("#", ns("r_code"))),
|
| 30 | -+ | ! |
- #' @export+ modalButton("Dismiss"),
|
| 31 | +! | +
+ style = "mb-4"+ |
+ |
| 32 |
- #' @rdname module_teal_with_splash+ ),+ |
+ ||
| 33 | +! | +
+ tags$div(tags$pre(id = ns("r_code"), rcode)),
|
|
| 32 | +34 |
- srv_teal_with_splash <- function(id, data, modules, filter = teal_slices()) {
+ ), |
|
| 33 | +35 | ! |
- lifecycle::deprecate_soft(+ title = title, |
| 34 | +36 | ! |
- when = "0.16",+ footer = tagList( |
| 35 | +37 | ! |
- what = "srv_teal_with_splash()",+ actionButton(ns("copyRCode"), "Copy to Clipboard", `data-clipboard-target` = paste0("#", ns("r_code"))),
|
| 36 | +38 | ! |
- details = "Deprecated, please use `srv_teal` instead"+ modalButton("Dismiss")
|
| 37 | +39 |
- )+ ), |
|
| 38 | +40 | ! |
- srv_teal(id = id, data = data, modules = modules, filter = filter)+ size = "l",+ |
+
| 41 | +! | +
+ easyClose = TRUE |
|
| 39 | +42 | ++ |
+ ))+ |
+
| 43 |
}@@ -47122,16 +45887,14 @@ teal coverage - 59.73% | ||
| 22 | -2x - | +2x |
packageStartupMessage( |
| 23 | -2x - | +2x |
"\nYou are using teal version ", |
@@ -47152,8 +45915,7 @@
| 26 | -2x - | +2x |
read.dcf(system.file("DESCRIPTION", package = "teal"))[, "Version"]
|
@@ -47252,14 +46014,14 @@
| 1 |
- #' Create a `teal` module for previewing a report+ #' Evaluate expression on `teal_data_module` |
|||
| 3 |
- #' @description `r lifecycle::badge("experimental")`
+ #' @details |
|||
| 4 |
- #'+ #' `within` is a convenience function for evaluating inline code inside the environment of a `teal_data_module`. |
|||
| 5 |
- #' This function wraps [teal.reporter::reporter_previewer_ui()] and+ #' It accepts only inline expressions (both simple and compound) and allows for injecting values into `expr` through |
|||
| 6 |
- #' [teal.reporter::reporter_previewer_srv()] into a `teal_module` to be+ #' the `...` argument: as `name:value` pairs are passed to `...`, `name` in `expr` will be replaced with `value.` |
|||
| 7 |
- #' used in `teal` applications.+ #' |
|||
| 8 |
- #'+ #' @param data (`teal_data_module`) object |
|||
| 9 |
- #' If you are creating a `teal` application using [init()] then this+ #' @param expr (`expression`) to evaluate. Must be inline code. See |
|||
| 10 |
- #' module will be added to your application automatically if any of your `teal_modules`+ #' @param ... See `Details`. |
|||
| 11 |
- #' support report generation.+ #' |
|||
| 12 |
- #'+ #' @return |
|||
| 13 |
- #' @inheritParams teal_modules+ #' `within` returns a `teal_data_module` object with a delayed evaluation of `expr` when the module is run. |
|||
| 14 |
- #' @param server_args (named `list`)+ #' |
|||
| 15 |
- #' Arguments passed to [teal.reporter::reporter_previewer_srv()].+ #' @examples |
|||
| 16 |
- #'+ #' within(tdm, dataset1 <- subset(dataset1, Species == "virginica")) |
|||
| 17 |
- #' @return+ #' |
|||
| 18 |
- #' `teal_module` (extended with `teal_module_previewer` class) containing the `teal.reporter` previewer functionality.+ #' # use additional parameter for expression value substitution. |
|||
| 19 |
- #'+ #' valid_species <- "versicolor" |
|||
| 20 |
- #' @export+ #' within(tdm, dataset1 <- subset(dataset1, Species %in% species), species = valid_species) |
|||
| 21 |
- #'+ #' @include teal_data_module.R |
|||
| 22 |
- reporter_previewer_module <- function(label = "Report previewer", server_args = list()) {
+ #' @name within |
|||
| 23 | -7x - | +
- checkmate::assert_string(label)+ #' @rdname teal_data_module |
||
| 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))))+ #' @export |
||
| 26 |
-
+ #' |
|||
| 27 | -3x - | +
- message("Initializing reporter_previewer_module")
+ within.teal_data_module <- function(data, expr, ...) {
|
||
| 28 | -+ | 2x |
-
+ expr <- substitute(expr) |
|
| 29 | -3x - | +2x |
- srv <- function(id, reporter, ...) {
+ extras <- list(...) |
|
| 30 | -! | +
- teal.reporter::reporter_previewer_srv(id, reporter, ...)+ |
||
| 31 |
- }+ # Add braces for consistency. |
|||
| 32 | -+ | 2x |
-
+ if (!identical(as.list(expr)[[1L]], as.symbol("{"))) {
|
|
| 33 | -3x - | -
- ui <- function(id, ...) {
- |
- ||
| 34 | -! | +2x |
- teal.reporter::reporter_previewer_ui(id, ...)+ expr <- call("{", expr)
|
|
| 35 | +34 |
} |
||
| 36 | +35 | |||
| 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 | -+ | 36 | +2x |
- )+ calls <- as.list(expr)[-1] |
| 42 | +37 |
- # Module is created with a placeholder label and the label is changed later.+ |
||
| 43 | +38 |
- # This is to prevent another module being labeled "Report previewer".- |
- ||
| 44 | -3x - | -
- class(module) <- c(class(module), "teal_module_previewer")+ # Inject extra values into expressions. |
||
| 45 | -3x - | +39 | +2x |
- module$label <- label+ calls <- lapply(calls, function(x) do.call(substitute, list(x, env = extras))) |
| 46 | -3x - | +|||
| 40 | +
- attr(module, "teal_bookmarkable") <- TRUE+ |
|||
| 47 | -3x - | +41 | +2x |
- module+ eval_code(object = data, code = as.expression(calls)) |
| 48 | +42 |
}@@ -47655,48 +46361,42 @@ teal coverage - 59.73% | ||
| 7 | -938x - | +969x |
if (!isTRUE(checkmate::test_class(x, classes = "reactive", null.ok = null.ok))) {
|
|
| 8 | -4x - | +4x |
cl <- class(x) |
|
| 9 | -4x - | +4x |
return(sprintf( |
|
| 10 | -4x - | +4x |
"Must be a reactive (i.e. inherit from 'reactive' class) but has class%s '%s'", |
|
| 11 | -4x - | +4x |
if (length(cl) > 1L) "es" else "", |
|
| 12 | -4x - | +4x |
paste0(cl, collapse = "','") |
@@ -47717,8 +46417,7 @@ |
| 15 | -934x - | +965x |
return(TRUE) |
@@ -47746,8 +46445,7 @@ |
| 19 | -29x - | +30x |
isTRUE(check_reactive(x, null.ok = null.ok)) |
@@ -47852,88 +46550,77 @@ |
| 34 | -40x - | +40x |
tryCatch( |
|
| 35 | -40x - | +40x |
x, |
|
| 36 | -40x - | +40x |
error = function(e) {
|
|
| 37 | -2x - | +2x |
stop( |
|
| 38 | -2x - | +2x |
"\n", |
|
| 39 | -2x - | +2x |
pre, |
|
| 40 | -2x - | +2x |
"\n", |
|
| 41 | -2x - | +2x |
e$message, |
|
| 42 | -2x - | +2x |
"\n", |
|
| 43 | -2x - | +2x |
post, |
|
| 44 | -2x - | +2x |
call. = FALSE |
@@ -47961,8 +46648,7 @@ |
| 48 | -38x - | +38x |
x |
@@ -47977,313 +46663,6 @@
| 1 | -- |
- #' Show `R` code modal- |
-
| 2 | -- |
- #'- |
-
| 3 | -- |
- #' @description `r lifecycle::badge("deprecated")`
- |
-
| 4 | -- |
- #'- |
-
| 5 | -- |
- #' Use the [shiny::showModal()] function to show the `R` code inside.- |
-
| 6 | -- |
- #'- |
-
| 7 | -- |
- #' @param title (`character(1)`)- |
-
| 8 | -- |
- #' Title of the modal, displayed in the first comment of the `R` code.- |
-
| 9 | -- |
- #' @param rcode (`character`)- |
-
| 10 | -- |
- #' vector with `R` code to show inside the modal.- |
-
| 11 | -- |
- #' @param session (`ShinySession`) optional- |
-
| 12 | -- |
- #' `shiny` session object, defaults to [shiny::getDefaultReactiveDomain()].- |
-
| 13 | -- |
- #'- |
-
| 14 | -- |
- #' @references [shiny::showModal()]- |
-
| 15 | -- |
- #' @export- |
-
| 16 | -- |
- show_rcode_modal <- function(title = NULL, rcode, session = getDefaultReactiveDomain()) {
- |
-
| 17 | -! | -
- lifecycle::deprecate_soft(- |
-
| 18 | -! | -
- when = "0.16",- |
-
| 19 | -! | -
- what = "show_rcode_modal()",- |
-
| 20 | -! | -
- details = "This function will be removed in the next release."- |
-
| 21 | -- |
- )- |
-
| 22 | -- | - - | -
| 23 | -! | -
- rcode <- paste(rcode, collapse = "\n")- |
-
| 24 | -- | - - | -
| 25 | -! | -
- ns <- session$ns- |
-
| 26 | -! | -
- showModal(modalDialog(- |
-
| 27 | -! | -
- tagList(- |
-
| 28 | -! | -
- tags$div(- |
-
| 29 | -! | -
- actionButton(ns("copyRCode"), "Copy to Clipboard", `data-clipboard-target` = paste0("#", ns("r_code"))),
- |
-
| 30 | -! | -
- modalButton("Dismiss"),
- |
-
| 31 | -! | -
- style = "mb-4"- |
-
| 32 | -- |
- ),- |
-
| 33 | -! | -
- tags$div(tags$pre(id = ns("r_code"), rcode)),
- |
-
| 34 | -- |
- ),- |
-
| 35 | -! | -
- title = title,- |
-
| 36 | -! | -
- footer = tagList(- |
-
| 37 | -! | -
- actionButton(ns("copyRCode"), "Copy to Clipboard", `data-clipboard-target` = paste0("#", ns("r_code"))),
- |
-
| 38 | -! | -
- modalButton("Dismiss")
- |
-
| 39 | -- |
- ),- |
-
| 40 | -! | -
- size = "l",- |
-
| 41 | -! | -
- easyClose = TRUE- |
-
| 42 | -- |
- ))- |
-
| 43 | -- |
- }- |
-