Feature branch PR #1253

- reactive data - initialize modules ui

…main

- mapping_matrix works - initializing filters works - restoring filters after data reload works

This reverts commit 6eb139e.

datasets 'verification_status' attribute is derived from teal_data

WIP file upload

filter_manager_panel

Adds bookmark module to the teal refactor --------- Signed-off-by: Vedha Viyash <[email protected]> Co-authored-by: go_gonzo <[email protected]> Co-authored-by: Dawid Kałędkowski <[email protected]>

see ?filter_manager

✖ (WIP) shinytest2

Signed-off-by: Marcin <[email protected]> Co-authored-by: go_gonzo <[email protected]> Co-authored-by: Dawid Kałędkowski <[email protected]>

Signed-off-by: Marcin <[email protected]>

… does not crash

Co-authored-by: André Veríssimo <[email protected]> Signed-off-by: Marcin <[email protected]>

```r ❯ checking R code for possible problems ... NOTE get_object_filter_overview_MultiAssayExperiment : get_experiment_keys: no visible binding for global variable 'colname' srv_data_summary : <anonymous>: no visible binding for global variable 'obs' srv_data_summary : <anonymous>: no visible binding for global variable 'obs_filtered' srv_data_summary : <anonymous>: no visible binding for global variable 'subjects' srv_data_summary : <anonymous>: no visible binding for global variable 'subjects_filtered' Undefined global functions or variables: colname obs obs_filtered subjects subjects_filtered ``` is a part of a NOTE https://github.com/insightsengineering/teal/actions/runs/9954607649/job/27500608846#step:24:103 that is on CHECK GitHub Action blocklist https://github.com/insightsengineering/teal/blob/main/.github/workflows/check.yaml#L33-L42 This PR provides a fix that replaces `transform()` and `subset()` with `$<-` and `[, ` operators. The documentation suggests that it should only be used in interactive mode #1267 (comment) --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

…#1270)

transform WIP

…in real-time in transformers

…rtUI@main

keep warning on console

- test transforms

Signed-off-by: Marcin <[email protected]> Co-authored-by: vedhav <[email protected]> Co-authored-by: Dawid Kałędkowski <[email protected]>

…ering/teal into 669_insertUI@main

Code is added manually to slot as it was safely calculated

- add method $slices_set to simplify hard-setting

…ronment.

.slicesGlobal: no visible global function definition for ‘new’

Merge branch '669_insertUI@main' of https://github.com/insightsengineering/teal into 669_insertUI@main # Conflicts: # R/1.0_filter_panel.R # man/dot-observe_active_filter_changed.Rd # man/module_filter_panel.Rd

…ering/teal into 669_insertUI@main

Can't approve PR created by myself - merging directly

1. modules receive datanames from `modules$datanames` 2. modules receive all datanames @env (except _raw) when `modules$dataname == "all"` and `@datanames == <empty>` 3. modules receive `@datanames` if `modules$dataname == "all"`

…1281) Part of #1253 --------- Co-authored-by: Vedha Viyash <[email protected]> Co-authored-by: vedhav <[email protected]>

Part of #1253 --------- Signed-off-by: Marcin <[email protected]> Co-authored-by: Dawid Kałędkowski <[email protected]>

…1283) Adds `teal_transform_module()` to be used to create data modules for transformation.

… a normal module (#1284) Changes: 1. Soft deprecates calling the `landing_popup_module` inside `modules` argument of `init` 2. Add a new `landing_popup` argument to `init` to accept this module. 3. Update the `TealAppDriver` to accept this new argument. --------- Signed-off-by: Vedha Viyash <[email protected]> Co-authored-by: Dawid Kałędkowski <[email protected]> Co-authored-by: go_gonzo <[email protected]>

@averissimo

) # Pull Request #### Fixes - teal.slices - after removal of the slice make sure that observers of FilterState are destroyed. To test - take an app with DDL. Add filter and reload data several times. After this try to remove filter with remove button. What is interesting that single FIlterState card remove button needs to be pushed several times (it removes old FIlterStates which are not rendered anymore) while remove-all seems to not add observers one over another (it is enough to click once). #### Needs Branch `teal_slice@669_insertUI@main` on `{teal.slices}` #### Changes description - Keeps previous FilteredDataset to safely clean the filter panel ##### How to test? 1. Run app below 2. Reload the dataset using the "`data` tab" 3. Remove individual filter from filter panel 4. Check if filter has been removed with a single click Repeat test without `module_specific = TRUE` ```r # teal.slices - # after removal of the slice make sure that observers of FilterState are destroyed. # # To test - take an app with DDL. # - Add filter # - reload data several times. # # After this try to remove filter with remove button. # What is interesting that single FIlterState card remove button needs to be # pushed several times (it removes old FIlterStates which are not rendered anymore) # while remove-all seems to not add observers one over another (it is enough to # click once). @averissimo # Possible bug: reloading data will clear default values of the initial filter state options( teal.log_level = "DEBUG", teal.show_js_log = TRUE, # teal.bs_theme = bslib::bs_theme(version = 5), shiny.bookmarkStore = "server" ) pkgload::load_all("../teal.slice") pkgload::load_all("../teal") data <- teal::teal_data_module( ui = function(id) { ns <- shiny::NS(id) shiny::tagList( shiny::textInput(ns("username"), label = "Username"), shiny::passwordInput(ns("password"), label = "Password"), shiny::actionButton(ns("submit"), label = "Submit") ) }, server = function(id, ...) { shiny::moduleServer(id, function(input, output, session) { shiny::eventReactive(input$submit, { data <- teal.data::teal_data() |> within( { logger::log_debug("Loading data...") ADSL <- teal.data::rADSL ADTTE <- teal.data::rADTTE iris <- iris CO2 <- CO2 factors <- names(Filter(isTRUE, vapply(CO2, is.factor, logical(1L)))) CO2[factors] <- lapply(CO2[factors], as.character) }, username = input$username, password = input$password ) join_keys(data) <- default_cdisc_join_keys[c("ADSL", "ADTTE")] teal.data::datanames(data) <- c("ADSL", "ADTTE", "iris", "CO2") data }) }) } ) teal::init( data = data, modules = teal::modules( teal::modules( label = "Group", teal::example_module() ) ), filter = teal::teal_slices( teal.slice::teal_slice("ADSL", "AGE", selected = c(18L, 65L)), module_specific = TRUE, teal.slice::teal_slice("ADSL", "SEX") ), title = "yada" ) |> shiny::runApp() ``` --------- Signed-off-by: André Veríssimo <[email protected]>

Part of #1253 Fixes #1287 This PR do not show `filter-panel` nor `data-summary` if a module has `datanames` set to NULL. Tested with <details><summary> `tm_front_page(show_metadata = FALSE)` </summary> ``` library(teal.modules.general) data <- teal_data() data <- within(data, { require(nestcolor) ADSL <- rADSL attr(ADSL, "metadata") <- list("Author" = "NEST team", "data_source" = "synthetic data") }) datanames(data) <- "ADSL" join_keys(data) <- default_cdisc_join_keys[datanames(data)] table_1 <- data.frame(Info = c("A", "B"), Text = c("A", "B")) table_2 <- data.frame(`Column 1` = c("C", "D"), `Column 2` = c(5.5, 6.6), `Column 3` = c("A", "B")) table_3 <- data.frame(Info = c("E", "F"), Text = c("G", "H")) table_input <- list( "Table 1" = table_1, "Table 2" = table_2, "Table 3" = table_3 ) app <- init( data = data, modules = modules( tm_front_page( header_text = c( "Important information" = "It can go here.", "Other information" = "Can go here." ), tables = table_input, additional_tags = HTML("Additional HTML or shiny tags go here <br>"), footnotes = c("X" = "is the first footnote", "Y is the second footnote"), show_metadata = FALSE ) ), header = tags$h1("Sample Application"), footer = tags$p("Application footer"), ) if (interactive()) { shinyApp(app$ui, app$server) } ```` </details> <details><summary> `tm_front_page(show_metadata = TRUE)` </summary> ``` library(teal.modules.general) data <- teal_data() data <- within(data, { require(nestcolor) ADSL <- rADSL attr(ADSL, "metadata") <- list("Author" = "NEST team", "data_source" = "synthetic data") }) datanames(data) <- "ADSL" join_keys(data) <- default_cdisc_join_keys[datanames(data)] table_1 <- data.frame(Info = c("A", "B"), Text = c("A", "B")) table_2 <- data.frame(`Column 1` = c("C", "D"), `Column 2` = c(5.5, 6.6), `Column 3` = c("A", "B")) table_3 <- data.frame(Info = c("E", "F"), Text = c("G", "H")) table_input <- list( "Table 1" = table_1, "Table 2" = table_2, "Table 3" = table_3 ) app <- init( data = data, modules = modules( tm_front_page( header_text = c( "Important information" = "It can go here.", "Other information" = "Can go here." ), tables = table_input, additional_tags = HTML("Additional HTML or shiny tags go here <br>"), footnotes = c("X" = "is the first footnote", "Y is the second footnote"), show_metadata = TRUE ) ), header = tags$h1("Sample Application"), footer = tags$p("Application footer"), ) if (interactive()) { shinyApp(app$ui, app$server) } ```` </details> <details><summary> `tm_a_pca` </summary> ``` library(teal.modules.general) library(teal.widgets) # general data example data <- teal_data() data <- within(data, { require(nestcolor) USArrests <- USArrests }) datanames(data) <- "USArrests" app <- init( data = data, modules = modules( tm_a_pca( "PCA", dat = data_extract_spec( dataname = "USArrests", select = select_spec( choices = variable_choices( data = data[["USArrests"]], c("Murder", "Assault", "UrbanPop", "Rape") ), selected = c("Murder", "Assault"), multiple = TRUE ), filter = NULL ), ggplot2_args = ggplot2_args( labs = list(subtitle = "Plot generated by PCA Module") ) ) ) ) if (interactive()) { shinyApp(app$ui, app$server) } ```` </details> # `tm_front_page(show_metadata = FALSE)` <img width="689" alt="no_metdata" src="https://github.com/user-attachments/assets/e376e384-ff31-431a-854d-1d05eff46666"> # `tm_front_page(show_metadata = TRUE)` For `show_metadata = TRUE` the `datanames` are set to `all` and the datasets are shown, as they are also visible in the `Show metadata` modal <img width="664" alt="metadata" src="https://github.com/user-attachments/assets/111924b4-0330-4770-b5ba-44c742a311e7"> # `tm_a_pca` <img width="667" alt="image" src="https://github.com/user-attachments/assets/594e77d8-d66e-4c02-b88f-196eea59bc50">

Added tests to check the two new features of the `teal_data_module`: 1. Now `teal_data_module` can have `once` argument. 2. The module tabs are disabled when `teal_data_module` is not loaded. --------- Signed-off-by: Vedha Viyash <[email protected]> Co-authored-by: Marcin <[email protected]>

…eactive_teal_data` (#1294) Part of #1253 Additionally, we could have a static message on the summary, instead of repeating it. ### Before vs. With this PR ![image](https://github.com/user-attachments/assets/1d4e52ec-e9a4-4dcd-8e1d-012ac9aed6df) #### With simple error (not in PR yet) Simple change with ```diff diff --git a/R/module_data_summary.R b/R/module_data_summary.R index 76947d58a..dadfff0dc 100644 --- a/R/module_data_summary.R +++ b/R/module_data_summary.R @@ -89,7 +89,7 @@ srv_data_summary <- function(id, teal_data) { output$table <- renderUI({ summary_table_out <- try(summary_table()) if (inherits(summary_table_out, "try-error")) { - stop(strip_style(conditionMessage(attr(summary_table_out, "condition")))) + stop("Data and/or filters have an error. See details on main panel.") } else { body_html <- apply( summary_table_out, ``` ![image](https://github.com/user-attachments/assets/f91f4fa3-78af-413f-a940-8080f876766a) --------- Signed-off-by: André Veríssimo <[email protected]> Co-authored-by: Dawid Kałędkowski <[email protected]>

Closes #1300

Changed the way how datanames are passed between teal_data instances

Changes: 1. Adds the section on how to place the transform UI in the custom position inside the module. 2. Formats the `_pkgdown.yml` file (No change made to the file, just styling) 3. Extend the `example_module()` to handle the selection when datasets change (This can happen when using DDL to change datasets completely, such an example will be added to `teal.gallery`) --------- Signed-off-by: Vedha Viyash <[email protected]> Co-authored-by: Marcin <[email protected]> Co-authored-by: m7pr <[email protected]> Co-authored-by: Dony Unardi <[email protected]>

Part of #1253 ### Changes description - `check_modules_datanames` returns a string and HTML generator for: - **string**: to be used with logger - **HTML**: function to be used in teal UI - Message is generated in the same way. This adds complexity, but is consistent - `c("one", "two", "three")` renders as "one, two and three" (note the comma and `and`) - In the module context it doesn't show the current module label <details> <summary>Sample app</summary> ```r options( teal.log_level = "TRACE", teal.show_js_log = TRUE, # teal.bs_theme = bslib::bs_theme(version = 5), shiny.bookmarkStore = "server" ) pkgload::load_all("teal.data") pkgload::load_all("teal.slice") pkgload::load_all("teal") my_transformers <- list( teal_transform_module( label = "reactive ADSL", ui = function(id) { ns <- NS(id) tagList( div("Some UI for transform (merge)"), actionButton(ns("btn"), "Reload data") ) }, server = function(id, data) { moduleServer(id, function(input, output, session) { eventReactive(input$btn, { data() }) }) } ), teal_transform_module( label = "Keep first 6 from IRIS", ui = function(id) { ns <- NS(id) div( span("Some UI for transform (1)"), textInput(ns("obs"), label = "Number of rows", value = 6) ) }, server = function(id, data) { moduleServer(id, function(input, output, session) { reactive({ req(data()) obs <- as.numeric(input$obs) if (!is.finite(obs)) stop("NOT NUMERIC.") within(data(), iris <- head(iris, n), n = as.numeric(input$obs)) }) }) } ), teal_transform_module( label = "Keep first 6 from ADTTE", ui = function(id) div("Some UI for transform 2"), server = function(id, data) { moduleServer(id, function(input, output, session) { reactive({ req(data()) within(data(), ADTTE <- head(ADTTE)) }) }) } ) ) data <- teal_data_module( once = FALSE, ui = function(id) { ns <- NS(id) tagList( numericInput(ns("obs"), "Number of observations to show", 1000), actionButton(ns("submit"), label = "Submit") ) }, server = function(id, ...) { moduleServer(id, function(input, output, session) { logger::log_trace("example_module_transform2 initializing.") eventReactive(input$submit, { data <- teal_data() |> within( { logger::log_trace("Loading data") ADSL <- head(teal.data::rADSL, n = n) ADTTE <- teal.data::rADTTE iris <- iris CO2 <- CO2 factors <- names(Filter(isTRUE, vapply(CO2, is.factor, logical(1L)))) CO2[factors] <- lapply(CO2[factors], as.character) }, n = as.numeric(input$obs) ) join_keys(data) <- default_cdisc_join_keys[c("ADSL", "ADTTE")] teal.data::datanames(data) <- c("ADSL", "ADTTE", "iris", "CO2") data }) }) } ) teal::init( data = data, modules = list( example_module("mod-1", datanames = "all"), example_module("mod-2", transformers = my_transformers, datanames = c("ADSL", "ADTTE", "iris", "elo")), modules( label = "sub-modules", example_module("mod-2-sub1", transformers = my_transformers, datanames = c("ADSL", "ADTTE", "iris", "elo", "elo2")), example_module("mod-2-sub2", transformers = my_transformers, datanames = c("ADSL", "ADTTE", "iris", "elo")) ), example_module("mod-2", transformers = my_transformers[2:3]) ), filter = teal_slices( teal_slice("ADSL", "SEX"), teal_slice("ADSL", "AGE", selected = c(18L, 65L)) ) ) |> runApp() ``` </details> ![image](https://github.com/user-attachments/assets/9a6c09a6-2ce4-4c2b-b7f6-0cce7ab8670c) ![image](https://github.com/user-attachments/assets/2b4a8dd1-f7e7-44f8-80d3-9cb45dd3909b)

- supersede tdata - set next version to 0.16 (at this moment)

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Feature branch PR #1253

Feature branch PR #1253

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